Glycan therapeutic compositions and related methods thereof

ABSTRACT

Preparations of glycan therapeutics, pharmaceutical compositions, dietary supplements and medical foods thereof are provided, and methods of using said glycan therapeutics, e.g. in cancer therapy.

CLAIM OF PRIORITY

This application is a Continuation of U.S. application Ser. No.17/099,412, filed Nov. 16, 2020, which is a Continuation of U.S.application Ser. No. 16/140,091, filed Sep. 24, 2018, now U.S. Pat. No.10,894,057, which is a Continuation of U.S. application Ser. No.15/568,243, filed Oct. 20, 2017, now abandoned, which a U.S. nationalphase application under 35 U.S.C. § 371 of International Application No.PCT/US2016/029082, filed Apr. 23, 2016, which claims priority to U.S.Application No. 62/278,333, filed Jan. 13, 2016; U.S. Application No.62/238,110, filed Oct. 6, 2015; U.S. Application No. 62/238,112, filedOct. 6, 2015; U.S. Application No. 62/216,995, filed Sep. 10, 2015; U.S.Application No. 62/216,997, filed Sep. 10, 2015; U.S. Application No.62/152,017, filed Apr. 23, 2015; U.S. Application No. 62/152,011, filedApr. 23, 2015; and U.S. Application No. 62/152,007, filed Apr. 23, 2015.The disclosure of each of the foregoing applications is incorporatedherein by reference in its entirety.

BACKGROUND OF THE INVENTION

Maintaining or restoring human health faces a large number of challengesmany of which result from the lack of effective treatment options. Thereis a continued need for novel therapies and treatment regimens.

SUMMARY OF THE INVENTION

Provided herein are preparations of glycan therapeutics andpharmaceutical compositions, medical foods and dietary supplementsthereof, and related methods, which have been found to be effective totreat a number of diseases, disorders or pathological conditions.

In a first aspect, the invention relates to methods of treating animmune imbalance in a human subject. Provided herein is a method oftreating an immune imbalance in a human subject, comprising:administering to the subject a pharmaceutical composition, a medicalfood or a dietary supplement comprising a glycan therapeuticpreparation, in an effective amount to treat the subject. Providedherein is a method of treating an immune imbalance in a human subject,comprising: administering to the subject a first agent comprising aglycan therapeutic preparation, optionally in combination with a secondagent or therapy. In one embodiment, the first agent is a pharmaceuticalcomposition. In one embodiment, the first agent is a medical food.

In one embodiment, the first agent is a dietary supplement. In oneembodiment, the second agent is an immunomodulatory agent. In oneembodiment, the second agent or therapy treats a second disease,disorder or pathological condition of the subject. In one embodiment,the first agent and the second agent are administered in an effectiveamount to treat the immune imbalance. In one embodiment, the first agentis administered in an effective amount to treat the immune imbalance andthe second agent is administered in an effective amount to treat thesecond disease, disorder or pathological condition of the subject. Inone embodiment, the second agent is a dietary fiber. In one embodiment,the second agent is a probiotic bacterium. In one embodiment, thecombination is administered to a subject who has been treated for animmune imbalance. In one embodiment, the combination is administered toa subject who has not been treated for an immune imbalance. In oneembodiment, the first agent is administered to a subject that has beentreated with the second agent. In one embodiment, the second agent isadministered to a subject that has been treated with the first agent. Inone embodiment, the first agent and the second agent are administeredconcurrently to a subject.

Provided herein is a method for reducing an infection and/or aninflammation in a subject having an immune imbalance, the methodcomprising administering to the subject a glycan therapeutic preparationin an effective amount to reduce the infection and/or an inflammation.

Provided herein is a method of modulating the composition and/ormetabolic activity of the intestinal bacterial community of a subjecthaving an immune imbalance, comprising administering to the subject aglycan therapeutic composition and, optionally, an anti- orpro-inflammatory agent in an amount effective to modulate the subject'simmune system. In one embodiment, the methods further compriseadministering a probiotic microorganism. In one embodiment, ashort-chain fatty acid (SCFA) is modulated. In one embodiment, the SCFAis one or more of acetate, propionate, butyrate, isovalerate, valerate,hexanoate, heptanoate, and octanoate. In one embodiment, the one or moreSCFA is reduced. In some embodiments, the one or more SCFA is increased.In one embodiment, administration of the composition modulates (e.g.stimulates) growth or activity of beneficial gut bacteria, e.g.,Bifidobacteria. In one embodiment, administration of the glycantherapeutic preparation modulates the growth or function of one or morebacterial taxa, including Bifidobacteria, Bifidobacteriales,Bacteroidales, Clostridiales, Parabacteroides, and Akkermansia. In oneembodiment, administration of the glycan therapeutic preparationmodulates the growth or function of one or more bacterial taxa,including Blautia, Bifidobacterium, Roseburia, Coprococcus,Lachnospiraceae, Faecalibacterium, Parabacteroides, and Ruminococcaceae.In one embodiment, one or more host pathways are modulated, includinginflammatory responses, complement, apoptosis, antigen presentation,oxidative stress, cell adhesion, cytoskeleton remodeling, Notchsignaling, Wnt signaling, and/or one or more of the metabolic pathwayslisted in Table 19 ((super or sub pathways or level of a metabolite). Inone embodiment, one or more bile acids are modulated. In one embodiment,the bile acid is a primary bile acid. In one embodiment, the bile acidis a secondary bile acid. In one embodiment, the bile acid is one ormore of glycodeoxycholic acid, glycolithocholic acid, alpha-muricholicacid, beta-muricholic acid, taurocholic acid, and taurochenodeoxycholicacid. In one embodiment, the bile acid is DCA (deoxycholic acid) and/orLCA (lithocholic acid). In one embodiment, the bile acid is increased.In one embodiment, the bile acid is decreased. In one embodiment,administration of the composition results in the modulation of one ormore biomarkers including Interleukin 10, Interleukin, 4, Interleukin13, and Interleukin 35. In one embodiment, administration of thecomposition results in the modulation of one or more biomarkersincluding C-reactive protein, interleukin-6, interleukin-8,interleukin-18, insulin, blood glucose, leptin, serum amyloid A, serumamyloid P, and tumor necrosis factor-alpha. In one embodiment, one ormore cytokine selected from TNF-α, IL-8, monocyte chemoattractingprotein 1 (MCP-1), TGF-β, IL-12, IFN-γ, IL-4, and IL-10 is modulated. Inone embodiment, administration of the composition results in a i) areduced immune response or ii) an enhanced immune response. In oneembodiment, the production or release of pro-inflammatory cytokines isdecreased. In one embodiment, the production or release ofpro-inflammatory cytokines is increased. In one embodiment, theproduction or release of anti-inflammatory cytokines is increased. Inone embodiment, the production or release of anti-inflammatory cytokinesis decreased.

Provided herein is a method of modulating the function and/or activityof a pathway of a subject having an immune imbalance, comprisingadministering to the subject a glycan therapeutic composition and,optionally as second agent. In one embodiment, a short-chain fatty acid(SCFA) is modulated. In one embodiment, the SCFA is one or more ofacetate, propionate, butyrate, isovalerate, valerate, hexanoate,heptanoate, and octanoate. In one embodiment, the one or more SCFA isreduced. In some embodiments, the one or more SCFA is increased. In oneembodiment, one or more pathways are modulated, including inflammatoryresponses, complement, apoptosis, antigen presentation, oxidativestress, cell adhesion, cytoskeleton remodeling, Notch signaling, Wntsignaling, and/or one or more of the metabolic pathways listed in Table19 ((super or sub pathways or level of a metabolite). In one embodiment,one or more bile acids are modulated. In one embodiment, the bile acidis a primary bile acid. In one embodiment, the bile acid is a secondarybile acid. In one embodiment, the bile acid is one or more ofglycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid,beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid.In one embodiment, the bile acid is DCA (deoxycholic acid) and/or LCA(lithocholic acid). In one embodiment, the bile acid is increased. Inone embodiment, the bile acid is decreased.

Provided herein is a method of treating a dysbiosis in a subject havingan immune imbalance comprising administering to the subject apharmaceutical composition comprising a glycan therapeutic preparationin an effective amount to treat the dysbiosis.

For any and all of the foregoing methods, in one embodiment, the immuneimbalance is a suppression of the subject's immune system. In oneembodiment, the subject exhibits a deficient immune-surveillance. In oneembodiment, the subject has a pathogenic infection. In one embodiment,the subject has a cancer. In one embodiment, the immune imbalance is anaberrant activation of the subject's immune system. In one embodiment,the subject has a inflammatory disease that increase the risk ofdeveloping a cancer. In one embodiment, the subject hasgraft-versus-host disease. In one embodiment, the subject has anautoimmune disease. In one embodiment, the subject has an inflammatorygastrointestinal disease. In one embodiment, the immune imbalance isacute. In one embodiment, the immune imbalance is chronic. In oneembodiment, the immune imbalance is local. In one embodiment, the immuneimbalance is systemic. In one embodiment, the immune imbalance isaccompanied by aberrant growth of a pathogenic cell. In one embodiment,the pathogenic cell is an intracellular pathogen, an extracellularpathogen, or a cancerous cell.

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the glycan therapeuticpreparation has an average degree of branching (DB) of at least 0.01,iv) at least 50% of the glycans in the preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, v) theratio of alpha- to beta-glycosidic bonds present in the glycans of thepreparation overall is between about 1:1 to about 5:1, or vi) anycombination of one, two, three, four or five of i), ii), iii), iv) andv).

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the branchedoligosaccharides comprise glucose, galactose, arabinose, mannose,fructose, xylose, fucose, or rhamnose glycan units, iv) the averagedegree of branching (DB) of the branched glycans in the glycantherapeutic preparation is between 0.01 and 0.3, v) at least 50% of theglycans in the glycan therapeutic preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, vi) theaverage DP of the glycan therapeutic preparation is between about DP6and about DP10, vii) the ratio of alpha- to beta-glycosidic bondspresent in the glycans of the glycan therapeutic preparation is betweenabout 1:1 to about 5:1, viii) the glycan therapeutic preparation has afinal solubility limit in water of at least about 60 Brix at 23° C., orix) any combination of one, two, three, or four, five, six, seven, oreight of i), ii), iii), iv), v), vi), vii), and viii).

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise one or more glycan units, iii) the branched glycanscomprise at least 1% of branched glycan units, iv) the branched glycanshave a degree of polymerization (DP) of between 2 and 30 glycan units,v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- toalpha-configuration, vi) the branched glycans comprise a mixture of betaand alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3),and (2-6); vii) the glycan therapeutic preparation comprises a mixtureof branched glycans and unbranched glycans, viii) the glycan therapeuticpreparation comprises a mixture of digestible and non-digestibleglycans, or ix) any combination of one, two, three, or four, five, six,seven, or eight of i), ii), iii), iv), v), vi), vii), and viii).

In a second aspect, the invention relates to methods of treating anutritional imbalance in a human subject. Provided herein is a method oftreating a nutritional imbalance in a human subject, comprising:administering to the subject a pharmaceutical composition, a medicalfood or a dietary supplement comprising a glycan therapeuticpreparation, in an effective amount to treat the subject.

Provided herein is a method of treating a nutritional imbalance in ahuman subject, comprising: administering to the subject a first agentcomprising a glycan therapeutic preparation, optionally in combinationwith a second agent or therapy. In one embodiment, the first agent is apharmaceutical composition. In one embodiment, the first agent is amedical food. In one embodiment, the first agent is a dietarysupplement. In one embodiment, the second agent is metabolism modulatingagent. In one embodiment, the second agent or therapy treats a seconddisease, disorder or pathological condition of the subject. In oneembodiment, the first agent and the second agent are administered in aneffective amount to treat the nutritional imbalance. In one embodiment,the first agent is administered in an effective amount to treat thenutritional imbalance and the second agent is administered in aneffective amount to treat the second disease, disorder or pathologicalcondition of the subject. In one embodiment, the second agent is adietary fiber. In one embodiment, the second agent is a probioticbacterium. In one embodiment, the combination is administered to asubject who has been treated for a nutritional imbalance. In oneembodiment, the combination is administered to a subject who has notbeen treated for a nutritional imbalance. In one embodiment, the firstagent is administered to a subject that has been treated with the secondagent. In one embodiment, the second agent is administered to a subjectthat has been treated with the first agent. In one embodiment, the firstagent and the second agent are administered concurrently to a subject.

Provided herein is a method for reducing an inflammation in a subjecthaving a nutritional imbalance, the method comprising administering tothe subject a glycan therapeutic preparation in an effective amount toreduce the inflammation.

Provided herein is a method of modulating the composition and/ormetabolic activity of the intestinal bacterial community of a subjecthaving a nutritional imbalance, comprising administering to the subjecta glycan therapeutic composition and an anti- or pro-inflammatory agentin an amount effective to modulate the subject's immune system. In oneembodiment, the methods further comprise administering a probioticmicroorganism. In one embodiment, a short-chain fatty acid (SCFA) ismodulated. In one embodiment, the SCFA is one or more of acetate,propionate, butyrate, isovalerate, valerate, hexanoate, heptanoate, andoctanoate. In one embodiment, the one or more SCFA is reduced. In someembodiments, the one or more SCFA is increased. In one embodiment,administration of the composition modulates (e.g. stimulates) growth oractivity of beneficial gut bacteria, e.g., Bifidobacteria. In oneembodiment, administration of the glycan therapeutic preparationmodulates the growth or function of one or more bacterial taxa,including Bifidobacteria, Bifidobacteriales, Bacteroidales,Clostridiales, Parabacteroides, and Akkermansia. In one embodiment,administration of the glycan therapeutic preparation modulates thegrowth or function of one or more bacterial taxa, including Blautia,Bifidobacterium, Roseburia, Coprococcus, Lachnospiraceae,Faecalibacterium, Parabacteroides, and Ruminococcaceae. In oneembodiment, one or more host pathways are modulated, includinginflammatory responses, complement, apoptosis, antigen presentation,oxidative stress, cell adhesion, cytoskeleton remodeling, Notchsignaling, Wnt signaling, and/or one or more of the metabolic pathwayslisted in Table 19 ((super or sub pathways or level of a metabolite). Inone embodiment, one or more bile acids are modulated. In one embodiment,the bile acid is a primary bile acid. In one embodiment, the bile acidis a secondary bile acid. In one embodiment, the bile acid is one ormore of glycodeoxycholic acid, glycolithocholic acid, alpha-muricholicacid, beta-muricholic acid, taurocholic acid, and taurochenodeoxycholicacid. In one embodiment, the bile acid is DCA (deoxycholic acid) and/orLCA (lithocholic acid). In one embodiment, the bile acid is increased.In one embodiment, the bile acid is decreased. In one embodiment,administration of the composition results in the modulation of one ormore biomarkers including Interleukin 10, Interleukin, 4, Interleukin13, and Interleukin 35. In one embodiment, administration of thecomposition results in the modulation of one or more biomarkersincluding C-reactive protein, interleukin-6, interleukin-8,interleukin-18, insulin, blood glucose, leptin, serum amyloid A, serumamyloid P, and tumor necrosis factor-alpha. In one embodiment, one ormore cytokine selected from TNF-α, IL-8, monocyte chemoattractingprotein 1 (MCP-1), TGF-β, IL-12, IFN-γ, IL-4, and IL-10 is modulated. Inone embodiment, administration of the composition results in a i) areduced immune response or ii) an enhanced immune response. In oneembodiment, the production or release of pro-inflammatory cytokines isdecreased. In one embodiment, the production or release ofpro-inflammatory cytokines is increased. In one embodiment, theproduction or release of anti-inflammatory cytokines is increased. Inone embodiment, the production or release of anti-inflammatory cytokinesis decreased.

Provided herein is a method of modulating the function and/or activityof a pathway of a subject having an nutritional imbalance, comprisingadministering to the subject a glycan therapeutic composition and,optionally as second agent. In one embodiment, a short-chain fatty acid(SCFA) is modulated. In one embodiment, the SCFA is one or more ofacetate, propionate, butyrate, isovalerate, valerate, hexanoate,heptanoate, and octanoate. In one embodiment, the one or more SCFA isreduced. In some embodiments, the one or more SCFA is increased. In oneembodiment, one or more pathways are modulated, including inflammatoryresponses, complement, apoptosis, antigen presentation, oxidativestress, cell adhesion, cytoskeleton remodeling, Notch signaling, Wntsignaling, and/or one or more of the metabolic pathways listed in Table19 ((super or sub pathways or level of a metabolite). In one embodiment,one or more bile acids are modulated. In one embodiment, the bile acidis a primary bile acid. In one embodiment, the bile acid is a secondarybile acid. In one embodiment, the bile acid is one or more ofglycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid,beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid.In one embodiment, the bile acid is DCA (deoxycholic acid) and/or LCA(lithocholic acid). In one embodiment, the bile acid is increased. Inone embodiment, the bile acid is decreased.

Provided herein is a method of treating a dysbiosis in a subject havinga nutritional imbalance comprising administering to the subject apharmaceutical composition comprising a glycan therapeutic preparationin an effective amount to treat the dysbiosis.

For any and all of the foregoing methods, in one embodiment, thenutritional imbalance is acute. In one embodiment, the nutritionalimbalance is chronic. In one embodiment, the subject has a metabolicdisease or syndrome. In one embodiment, the subject has a wastingsyndrome. In one embodiment, the wasting syndrome is cachexia. In oneembodiment, the subject has cancer. In one embodiment, the cancer is agastrointestinal cancer. In one embodiment, the cancer is anon-gastrointestinal cancer.

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the glycan therapeuticpreparation has an average degree of branching (DB) of at least 0.01,iv) at least 50% of the glycans in the preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, v) theratio of alpha- to beta-glycosidic bonds present in the glycans of thepreparation overall is between about 1:1 to about 5:1, or vi) anycombination of one, two, three, four or five of i), ii), iii), iv) andv).

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the branchedoligosaccharides comprise glucose, galactose, arabinose, mannose,fructose, xylose, fucose, or rhamnose glycan units, iv) the averagedegree of branching (DB) of the branched glycans in the glycantherapeutic preparation is between 0.01 and 0.3, v) at least 50% of theglycans in the glycan therapeutic preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, vi) theaverage DP of the glycan therapeutic preparation is between about DP6and about DP10, vii) the ratio of alpha- to beta-glycosidic bondspresent in the glycans of the glycan therapeutic preparation is betweenabout 1:1 to about 5:1, viii) the glycan therapeutic preparation has afinal solubility limit in water of at least about 60 Brix at 23° C., orix) any combination of one, two, three, or four, five, six, seven, oreight of i), ii), iii), iv), v), vi), vii), and viii).

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise one or more glycan units, iii) the branched glycanscomprise at least 1% of branched glycan units, iv) the branched glycanshave a degree of polymerization (DP) of between 2 and 30 glycan units,v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- toalpha-configuration, vi) the branched glycans comprise a mixture of betaand alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3),and (2-6); vii) the glycan therapeutic preparation comprises a mixtureof branched glycans and unbranched glycans, viii) the glycan therapeuticpreparation comprises a mixture of digestible and non-digestibleglycans, or ix) any combination of one, two, three, or four, five, six,seven, or eight of i), ii), iii), iv), v), vi), vii), and viii).

In a third aspect, the invention relates to methods of treating cancerin a human subject. Provided herein is a method of treating cancer in ahuman subject, comprising: administering to the subject a pharmaceuticalcomposition, a medical food or a dietary supplement comprising a glycantherapeutic preparation, in an effective amount to treat the subject.

Provided herein is a method of treating cancer in a human subject,comprising: administering to the subject a first agent comprising aglycan therapeutic preparation, optionally in combination with a secondagent or therapy.

In one embodiment, the first agent is a pharmaceutical composition. Inone embodiment, the first agent is a medical food. In one embodiment,the first agent is a dietary supplement. In one embodiment, the secondagent is a checkpoint modulator, a cancer vaccine, an anti-cancerbiologic, or a chemotherapeutic agent. In one embodiment, the immunecheckpoint inhibitor is an antibody, a fusion protein, or a smallmolecule. In one embodiment, the cancer vaccine is a tumor cell vaccine,an antigen vaccine, a dendritic cell vaccine, a DNA vaccine, or a vectorbased vaccine. In one embodiment, the anti-cancer biologic is a cytokineor an antibody. In one embodiment, the chemotherapeutic agent is analkylating agent, an antimetabolite, a folic acid analog, a pyrimidineanalog, a purine analog, a vinca alkaloid, an epipodopyyllo toxin, anantibiotic, L-asparaginase, a topoisomerase inhibitor, an interferon, aplatinum coordination complex, anthracenedione substituted urea, amethyl hydrazine derivative, an adrenocortical suppressant, anadrenocorticosteroid, a progestin, an estrogen, an anti-estrogen, anandrogen, an anti-androgen, or a gonadotropin-releasing hormone analog.In one embodiment, the second therapy is adoptive T cell therapy, NKcell therapy, or a non drug treatment. In one embodiment, the non-drugtreatment is radiation therapy, cryotherapy, hyperthermia or surgicalexcision of tumor tissue. In one embodiment, the adoptive T cell therapycomprises administering autologous and/or allogeneic T-cells. In oneembodiment, the second agent is a dietary fiber. In one embodiment, thesecond agent is a probiotic bacterium. In one embodiment, thecombination is administered to a subject who has been treated with ananti-cancer therapy. In one embodiment, the combination is administeredto a subject who has not been treated with an anti-cancer therapy. Inone embodiment, the first agent is administered to a subject that hasbeen treated with the second agent. In one embodiment, the second agentis administered to a subject that has been treated with the first agent.In one embodiment, the first agent and the second agent are administeredconcurrently to a subject.

Provided herein is a method of modulating the composition and/ormetabolic activity of the intestinal bacterial community of a subjecthaving cancer, comprising administering to the subject a glycantherapeutic composition and an anti- or pro-inflammatory agent in anamount effective to modulate the subject's immune system. In oneembodiment, the methods further comprise administering an anti-canceragent. In one embodiment, the methods further comprise administering aprobiotic microorganism. In one embodiment, a short-chain fatty acid(SCFA) is modulated. In one embodiment, the SCFA is one or more ofacetate, propionate, butyrate, isovalerate, valerate, hexanoate,heptanoate, and octanoate. In one embodiment, the one or more SCFA isreduced. In some embodiments, the one or more SCFA is increased. In oneembodiment, administration of the composition results in induction ofapoptosis of cancer and precancerous cells in the subject. In oneembodiment, administration of the composition modulates (e.g.stimulates) growth or activity of beneficial gut bacteria, e.g.,Bifidobacteria. In one embodiment, administration of the glycantherapeutic preparation modulates the growth or function of one or morebacterial taxa, including Bifidobacteria, Bifidobacteriales,Bacteroidales, Clostridiales, Parabacteroides, and Akkermansia. In oneembodiment, administration of the glycan therapeutic preparationmodulates the growth or function of one or more bacterial taxa,including Blautia, Bifidobacterium, Roseburia, Coprococcus,Lachnospiraceae, Faecalibacterium, Parabacteroides, and Ruminococcaceae.In one embodiment, one or more host pathways are modulated, includinginflammatory responses, complement, apoptosis, antigen presentation,oxidative stress, cell adhesion, cytoskeleton remodeling, Notchsignaling, Wnt signaling, and/or one or more of the metabolic pathwayslisted in Table 19 ((super or sub pathways or level of a metabolite). Inone embodiment, one or more bile acids are modulated. In one embodiment,the bile acid is a primary bile acid. In one embodiment, the bile acidis a secondary bile acid. In one embodiment, the bile acid is one ormore of glycodeoxycholic acid, glycolithocholic acid, alpha-muricholicacid, beta-muricholic acid, taurocholic acid, and taurochenodeoxycholicacid. In one embodiment, the bile acid is DCA (deoxycholic acid) and/orLCA (lithocholic acid). In one embodiment, the bile acid is increased.In one embodiment, the bile acid is decreased. In one embodiment,administration of the composition results in the modulation of one ormore biomarkers including Interleukin 10, Interleukin, 4, Interleukin13, and Interleukin 35. In one embodiment, administration of thecomposition results in the modulation of one or more biomarkersincluding C-reactive protein, interleukin-6, interleukin-8,interleukin-18, insulin, blood glucose, leptin, serum amyloid A, serumamyloid P, and tumor necrosis factor-alpha. In one embodiment, one ormore cytokine selected from TNF-α, IL-8, monocyte chemoattractingprotein 1 (MCP-1), TGF-β, IL-12, IFN-γ, IL-4, and IL-10 is modulated. Inone embodiment, administration of the composition results in a i) areduction of intestinal cancer, and/or ii) an enhanced immune response.In one embodiment, the production or release of pro-inflammatorycytokines is decreased. In one embodiment, the production or release ofanti-inflammatory cytokines is increased.

Provided herein is a method of modulating the function and/or activityof a pathway of a subject having an immune imbalance, comprisingadministering to the subject a glycan therapeutic composition and,optionally as second agent. In one embodiment, a short-chain fatty acid(SCFA) is modulated. In one embodiment, the SCFA is one or more ofacetate, propionate, butyrate, isovalerate, valerate, hexanoate,heptanoate, and octanoate. In one embodiment, the one or more SCFA isreduced. In some embodiments, the one or more SCFA is increased. In oneembodiment, one or more pathways are modulated, including inflammatoryresponses, complement, apoptosis, antigen presentation, oxidativestress, cell adhesion, cytoskeleton remodeling, Notch signaling, Wntsignaling, and/or one or more of the metabolic pathways listed in Table19 ((super or sub pathways or level of a metabolite). In one embodiment,one or more bile acids are modulated. In one embodiment, the bile acidis a primary bile acid. In one embodiment, the bile acid is a secondarybile acid. In one embodiment, the bile acid is one or more ofglycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid,beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid.In one embodiment, the bile acid is DCA (deoxycholic acid) and/or LCA(lithocholic acid). In one embodiment, the bile acid is increased. Inone embodiment, the bile acid is decreased.

Provided herein is a method of treating a dysbiosis in a subject havingcancer comprising administering to the subject a pharmaceuticalcomposition comprising a glycan therapeutic preparation in an effectiveamount to treat the dysbiosis. In one embodiment, the subject undergoesan anti-cancer therapy. In one embodiment, the cancer therapy. In oneembodiment, the cancer therapy is a non-drug therapy. In one embodiment,the subject undergoes pain management therapy for cancer pain. In oneembodiment, the pain management therapy comprises administering opioids.In one embodiment, the subject exhibits constipation. In one embodiment,the constipation is acute. In one embodiment, the constipation ischronic. In one embodiment, the subject exhibits diarrhea. In oneembodiment, the diarrhea is acute. In one embodiment, the diarrhea ischronic.

Provided herein is a method for reducing an infection and/or aninflammation in a subject having cancer, the method comprisingadministering to the subject a glycan therapeutic preparation in aneffective amount to reduce the infection and/or an inflammation.

Provided herein is a method for inducing apoptosis of a cancer or aprecancerous cell in the subject having cancer, the method comprisingadministering to the subject a glycan therapeutic preparation in aneffective amount to induce apoptosis of the cancer or precancerous cell.

In one embodiment, the cancer is colon cancer or liver cancer. In oneembodiment, the glycan therapeutic preparation is administered incombination with another agent or therapy. In one embodiment, the otheragent or therapy is selected from radiation and chemotherapy andantibiotic therapy. In one embodiment, the other agent is selected froma probiotic, a prebiotic dietary fiber, an antibacterial agent, ananti-inflammatory agent, or an anti-cancer agent. In one embodiment, oneor more genes or gene products selected from Jun, Myc, Fos, Adamts1,ATF3, DDit4, Egr1, Sox9, IL1a, Gadd45b, and Gadd45g are modulated.

Provided herein is a method of reducing the risk of cancer in a subjectcomprising administering to the subject a glycan therapeutic preparationin an effective amount to promote a healthy microbiota in the subject,thereby reducing the cancer risk in the subject.

In one embodiment, the cancer is selected from breast cancer, ovariancancer, osteosarcoma, cervical cancer, lung cancer, bladder cancer,pancreatic cancer, prostate cancer, or melanoma. In one embodiment, theglycan therapeutic preparation is administered in combination withanother agent or therapy. In one embodiment, the other agent or therapyis selected from radiation and chemotherapy and antibiotic therapy. Inone embodiment, the other agent is selected from a probiotic, aprebiotic dietary fiber, an antibacterial agent, an anti-inflammatoryagent, or an anti-cancer agent. In one embodiment, the healthymicrobiota comprises microbial strains selected from Bacteroides,Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus,Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium,Roseburia, Prevotella, Bifidobacterium, Lactobacilli, Christensenellaminuta, or a Christensenellaceae species, Streptococcus thermophilus,Enterococcus and Bacillus species, E. coli, and Sacharomyces boulardii.

Provided herein is a method of modulating the composition of theintestinal bacterial community of a subject having cancer, comprisingadministering to the subject a glycan therapeutic preparation and ananti-cancer agent, in an amount effective to stimulate the growth ofbeneficial bacteria in the digestive system.

Provided herein is a method of modulating the metabolic activity of theintestinal bacterial community of a subject having cancer, comprisingadministering to the subject a glycan therapeutic composition and ananti-cancer agent, in an amount effective to modulate the metabolicactivity of beneficial bacteria in the digestive system. In oneembodiment, the metabolic activity is one or more of those listed inTable 19 ((super or sub pathways or level of a metabolite). In oneembodiment, the methods further comprise administering ananti-inflammatory agent. In one embodiment, the methods further compriseadministering a probiotic microorganism. In one embodiment, thebeneficial bacteria are selected from one or more of: Bacteroides,Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus,Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium,Roseburia, Prevotella, Bifidobacterium, Lactobacilli, Christensenellaminuta, and Christensenellaceae. In one embodiment, the beneficialbacteria include bifidobacterium. In one embodiment, a beneficial gutbacterial microbiota is disturbed. In one embodiment, the cancer iscolon or liver cancer.

In one embodiment, the expression of an oncogene is repressed. In oneembodiment, the oncogene is one of: jun, myc and fos. In one embodiment,the glycan therapeutic composition is labeled as a medical food. In oneembodiment, the method further comprises changes in the diet of thesubject. In one embodiment, the change is one or more of: i) increasingdietary fiber intake, ii) eliminating gastrointestinal stimulants, iii)administering anticholinergic medications before meals. In oneembodiment, the method further comprises one or more of: i) takinganxiety reducing measures, ii) regular exercise, iii) counseling foranxiety or depression. In one embodiment, the method further comprisesidentifying risk factors for developing a GI-related disease, todiagnose a GI-related disease, to evaluate the prognosis or severity ofsaid disease, to evaluate the success of a treatment regimen, or anycombination thereof, and wherein the GI related disease is cancer. Inone embodiment, identifying the risk factors comprises acquiring themetabolite profile of a subject's tissue sample or microbial culturefrom the subject's tissue. In one embodiment, the metabolite for thepurposes of diagnosis, prognostic risk assessment, or treatmentassessment includes short chain fatty acids, bile acids, and lactate andthose listed in Table 2. In one embodiment, the bile acid is a primarybile acid. In one embodiment, the bile acid is a secondary bile acid. Inone embodiment, the bile acid is one or more of glycodeoxycholic acid,glycolithocholic acid, alpha-muricholic acid, beta-muricholic acid,taurocholic acid, and taurochenodeoxycholic acid. In one embodiment, thebile acid is DCA (deoxycholic acid) and/or LCA (lithocholic acid). Inone embodiment, the bile acid is increased. In one embodiment, the bileacid is decreased.

For any and all of the foregoing methods, in one embodiment, the canceris a primary or non-metastatic tumor. In one embodiment, the cancer is ametastatic or a metastasized tumor. In one embodiment, the cancer is asolid cancer. In one embodiment, the cancer is a liquid cancer. In oneembodiment, the cancer is an immunogenic cancer. In one embodiment, theimmunogenic cancer comprises one or more of the followingcharacteristics: (a) tumor infiltrating lymphocytes (TIL), (b) somaticmutations, (c) neoantigens, (d) tertiary lymphoid structures; (e) highexpression of inflammatory gene expression, or (f) immune cellsexhibiting immunosuppressive phenotype. In one embodiment, the cancer isa gastrointestinal cancer. In one embodiment, the gastrointestinalcancer is colorectal cancer, pancreatic cancer, gastric cancer,oesophageal cancer, hepatocellular cancer, cholangiocellular cancer,oral cancer, or lip cancer. In one embodiment, the cancer is anon-gastrointestinal cancer. In one embodiment, the non-gastrointestinalcancer is a urogenital cancer, a gynecological cancer, a lung cancer, ahead and neck cancer, a CNS cancer, a malignant mesothelioma; a breastcancer, a skin cancer, a thyroid cancer; a bone and soft tissue sarcoma;or a hematologic neoplasia. In one embodiment, the urogenital cancer isa hormone sensitive prostate cancer, a hormone refractory prostatecancer, a renal cell cancer, a bladder cancer, or a penile cancer. Inone embodiment, the gynecological cancer is an ovarian cancer, acervical cancer, an endometrial cancer. In one embodiment, the lungcancer is a small-cell lung cancer or a non-small-cell lung cancer. Inone embodiment, the head and neck cancer is a squamous cell cancer. Inone embodiment, the CNS cancer is a malignant glioma, an astrocytomas, aretinoblastoma or a brain metastasis. In one embodiment, the breastcancer is a hormone refractory metastatic breast cancer. In oneembodiment, the skin cancer is a malignant melanoma, a basal andsquamous cell skin cancer, a Merkel cell carcinoma, a lymphoma of theskin, or Kaposi Sarcoma. In one embodiment, the hematologic neoplasia isa multiple myeloma, an acute myelogenous leukemia, a chronic myelogenousleukemia, a myelodysplastic syndrome, an acute lymphoblastic leukemia,or Hodgkin's lymphoma.

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the glycan therapeuticpreparation has an average degree of branching (DB) of at least 0.01,iv) at least 50% of the glycans in the preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, v) theratio of alpha- to beta-glycosidic bonds present in the glycans of thepreparation overall is between about 1:1 to about 5:1, or vi) anycombination of one, two, three, four or five of i), ii), iii), iv) andv).

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the branchedoligosaccharides comprise glucose, galactose, arabinose, mannose,fructose, xylose, fucose, or rhamnose glycan units, iv) the averagedegree of branching (DB) of the branched glycans in the glycantherapeutic preparation is between 0.01 and 0.3, v) at least 50% of theglycans in the glycan therapeutic preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, vi) theaverage DP of the glycan therapeutic preparation is between about DP6and about DP10, vii) the ratio of alpha- to beta-glycosidic bondspresent in the glycans of the glycan therapeutic preparation is betweenabout 1:1 to about 5:1, viii) the glycan therapeutic preparation has afinal solubility limit in water of at least about 60 Brix at 23° C., orix) any combination of one, two, three, or four, five, six, seven, oreight of i), ii), iii), iv), v), vi), vii), and viii).

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise one or more glycan units, iii) the branched glycanscomprise at least 1% of branched glycan units, iv) the branched glycanshave a degree of polymerization (DP) of between 2 and 30 glycan units,v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- toalpha-configuration, vi) the branched glycans comprise a mixture of betaand alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3),and (2-6); vii) the glycan therapeutic preparation comprises a mixtureof branched glycans and unbranched glycans, viii) the glycan therapeuticpreparation comprises a mixture of digestible and non-digestibleglycans, or ix) any combination of one, two, three, or four, five, six,seven, or eight of i), ii), iii), iv), v), vi), vii), and viii) . . . .

In a fourth aspect, the invention relates to methods of treatingsubjects with a glycan therapeutic preparation that also receive asecond treatment or therapy and methods of selecting subjects fortreatment. Provided herein is a method of treating a subject comprising:a) administering a pharmaceutical composition comprising a glycantherapeutic preparation to a subject who has been treated with a secondtreatment or therapy, b) administering a second treatment or therapy toa subject who has been treated with a pharmaceutical compositioncomprising a glycan therapeutic preparation, or c) administering apharmaceutical composition comprising a glycan therapeutic preparationand administering a second treatment or therapy to a subject.

In one embodiment, the treatment or therapy is an anti-cancer treatmentor therapy. In one embodiment, the treatment or therapy is a treatmentfor nutritional imbalance. In one embodiment, the treatment or therapyis a treatment for immune imbalance.

Provided herein is a method of selecting a subject for a treatment,comprising: (a) identifying a subject who has a disease, disorder orpathological condition, and (b) selecting the identified subject fortreatment with a glycan therapeutic preparation.

In one embodiment, the disease, disorder or pathological condition iscancer. In one embodiment, the disease, disorder or pathologicalcondition is nutritional imbalance. In one embodiment, the disease,disorder or pathological condition is immune imbalance. In oneembodiment, the step of selecting is carried out on the basis that theglycan therapeutic preparation will provide therapeutic benefit to thesubject. In one embodiment, the step of selecting is carried out on thebasis that the subject will or is expected to benefit fromadministration of the glycan therapeutic preparation. In one embodiment,the subject is treatment naïve. In one embodiment, the subject hasreceived anti-cancer treatment or therapy. In one embodiment, thesubject has received treatment for nutritional imbalance. In oneembodiment, the subject has received treatment for immune imbalance. Inone embodiment, the method further comprises assessing the subject'sgastrointestinal microbiota. In one embodiment, the assessment iscarried out before, during and/or after the treatment. In oneembodiment, treatment with a glycan therapeutic preparation modulatesthe abundance of a bacterial taxa. In one embodiment, the glycantherapeutic preparation is administered in an amount and for a timeeffective to result in shifted or modulated bacterial taxa in thesubject's gastrointestinal microbiota. In one embodiment, the taxa areone or more of Bifidobacteria, Bacterioides and Akkermansia. In oneembodiment, the taxa are of one or more of Bifidobacteria,Bifidobacteriales, Bacteroidales, Clostridiales, Parabacteroides, andAkkermansia. In one embodiment, the taxa are one or more of Blautia,Bifidobacterium, Roseburia, Coprococcus, Lachnospiraceae,Faecalibacterium, Parabacteroides, and Ruminococcaceae. In oneembodiment, the treatment results in increased levels of Th17 or Th1cells in the subject. In one embodiment, the method further comprisesidentifying risk factors for developing a cancer or second disease ordisorder, to diagnose a cancer or second disease or disorder, toevaluate the prognosis or severity of the a cancer or second disease ordisorder, to evaluate the success of a treatment regimen, or anycombination thereof. In one embodiment, identifying the risk factorscomprises acquiring the metabolite profile of a subject's tissue sampleor microbial culture from the subject's tissue. In one embodiment, themetabolite for the purposes of diagnosis, prognostic risk assessment, ortreatment assessment includes short chain fatty acids, bile acids, andlactate and the metabolites listed in Table 2. In one embodiment, thebile acid is a primary bile acid. In one embodiment, the bile acid is asecondary bile acid. In one embodiment, the bile acid is one or more ofglycodeoxycholic acid, glycolithocholic acid, alpha-muricholic acid,beta-muricholic acid, taurocholic acid, and taurochenodeoxycholic acid.In one embodiment, the bile acid is DCA (deoxycholic acid) and/or LCA(lithocholic acid). In one embodiment, the bile acid is increased. Inone embodiment, the bile acid is decreased. In one embodiment, themethod further comprises changes in the diet of the subject. In oneembodiment, the change is one or more of: i) increasing dietary fiberintake, ii) eliminating gastrointestinal stimulants, iii) administeringanticholinergic medications before meals. In one embodiment, the methodfurther comprises one or more of: i) taking anxiety reducing measures,ii) regular exercise, iii) counseling for anxiety or depression.

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the glycan therapeuticpreparation has an average degree of branching (DB) of at least 0.01,iv) at least 50% of the glycans in the preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, v) theratio of alpha- to beta-glycosidic bonds present in the glycans of thepreparation overall is between about 1:1 to about 5:1, or vi) anycombination of one, two, three, four or five of i), ii), iii), iv) andv).

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the branchedoligosaccharides comprise glucose, galactose, arabinose, mannose,fructose, xylose, fucose, or rhamnose glycan units, iv) the averagedegree of branching (DB) of the branched glycans in the glycantherapeutic preparation is between 0.01 and 0.3, v) at least 50% of theglycans in the glycan therapeutic preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, vi) theaverage DP of the glycan therapeutic preparation is between about DP6and about DP10, vii) the ratio of alpha- to beta-glycosidic bondspresent in the glycans of the glycan therapeutic preparation is betweenabout 1:1 to about 5:1, viii) the glycan therapeutic preparation has afinal solubility limit in water of at least about 60 Brix at 23° C., orix) any combination of one, two, three, or four, five, six, seven, oreight of i), ii), iii), iv), v), vi), vii), and viii).

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise one or more glycan units, iii) the branched glycanscomprise at least 1% of branched glycan units, iv) the branched glycanshave a degree of polymerization (DP) of between 2 and 30 glycan units,v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- toalpha-configuration, vi) the branched glycans comprise a mixture of betaand alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3),and (2-6); vii) the glycan therapeutic preparation comprises a mixtureof branched glycans and unbranched glycans, viii) the glycan therapeuticpreparation comprises a mixture of digestible and non-digestibleglycans, or ix) any combination of one, two, three, or four, five, six,seven, or eight of i), ii), iii), iv), v), vi), vii), and viii).

In a fifth aspect, the invention relates to methods of treating symptomsof a treatment or therapy, such as, e.g., toxicity symptoms in a humansubject. Provided herein is a method of reducing a symptom of atreatment or therapy, in a subject, comprising a) administering apharmaceutical composition comprising a glycan therapeutic preparationto a subject who has received the treatment or therapy; b) administeringthe treatment or therapy to a subject who has been treated with apharmaceutical composition comprising a glycan therapeutic preparation;or c) administering a pharmaceutical composition comprising a glycantherapeutic preparation and administering the treatment or therapy to asubject, thereby reducing a symptom of the treatment or therapy in thesubject.

In one embodiment, the treatment or therapy is an anti-cancer treatmentor therapy. In one embodiment, the treatment or therapy is a treatmentfor nutritional imbalance. In one embodiment, the treatment or therapyis a treatment for immune imbalance. In one embodiment, the symptom is aside-effect of the treatment or therapy. In one embodiment, the onset ofthe symptom is prior to administration of the glycan therapeuticpreparation. In one embodiment, the glycan therapeutic preparation isadministered after onset of the symptom. In one embodiment, the symptomof the treatment or therapy is unwanted. In one embodiment, the symptomis a gastrointestinal symptom. In one embodiment, the symptom is adigestive abnormality. In one embodiment, the gastrointestinal symptomis one or more of abdominal pain, cramping, nausea, vomiting, upsetstomach, gas, bloating, flatulence, diarrhea, constipation, heartburn,mucositis, and weight-gain, weight loss. In one embodiment, the symptomis a non-gastrointestinal symptom. In one embodiment, thenon-gastrointestinal symptom is one or more of anxiety, fear,depression, mental fog, dermatitis, chest pain, shortness of breath. Inone embodiment, the symptom is concurrent with or the result of ananti-cancer treatment or therapy. In one embodiment, the symptom isconcurrent with or the result of a treatment for nutritional imbalance.In one embodiment, the symptom is concurrent with or the result of atreatment for immune imbalance. In one embodiment, the symptom is one ormore of radiation injury pain, surgical pain, phantom pain, acute pain,chronic or persistent pain, breakthrough pain, peripheral neuropathy,stomatitis, mucositis, nausea, vomiting, diarrhea, constipation, urinaryincontinence, fatigue, anemia, lymphedema, infection, anxiety, fear,depression, fertility defect, and increased risk of developing a secondcancer. In one embodiment, the symptom is malnutrition or cachexia. Inone embodiment, the symptom is mucositis. In one embodiment, themucositisis is oral mucositis. In one embodiment, the mucositis isassociated with chemotherapy treatment or radiation therapy. In oneembodiment, the symptom is dose-limiting for the drug treatment ortherapy, thereby preventing the subject from being treated with themaximal efficacious dose of a drug.

Provided herein is a method of reducing toxicity of a drug treatment ina subject in need thereof comprising: a) administering a pharmaceuticalcomposition comprising a glycan therapeutic preparation to a subject whohas received the drug treatment; b) administering the drug treatment toa subject who has been treated with a pharmaceutical compositioncomprising a glycan therapeutic preparation; or c) administering apharmaceutical composition comprising a glycan therapeutic preparationand administering the drug treatment to a subject, in an effectiveamount to treat the subject.

In one embodiment, the drug treatment comprises administering animmunomodulatory drug. In one embodiment, the drug treatment comprisesadministering a metabolism modulatory drug. In one embodiment, the drugtreatment comprises administering an anti-cancer drug. In oneembodiment, the anti-cancer drug is irinotecan or 5-fluorouracil. In oneembodiment, the toxicity is a dose-limiting toxicity, thereby preventingthe subject from being treated with the maximal efficacious dose of adrug. In one embodiment, tolerance of the subject to drug treatment isincreased to a dose exceeding a sub-efficacious dose. In one embodiment,tolerance of the subject to drug treatment is increased to a dose equalto or exceeding the maximal efficacious dose of a drug in the subject.In one embodiment, the methods further comprise administering apharmaceutical composition comprising a glycan therapeutic preparationto a subject who has received a first treatment, and optionally,providing a second treatment, e.g., wherein the second treatmentcomprises administration of the drug or therapy at a higher dosage, atmore frequent intervals, at a higher total of individualadministrations, providing a higher Cmax, providing a higher troughlevel, etc., than the prior treatment. In one embodiment, the methodsfurther comprise providing a subsequent treatment to a subject who hasreceived a pharmaceutical composition comprising a glycan therapeuticpreparation and received the first treatment, wherein the secondtreatment comprises administration of the drug or therapy at a higherdosage, at more frequent intervals, at a higher total of individualadministrations, providing a higher Cmax, providing a higher troughlevel, etc., than the prior treatment. In one embodiment, the methodsfurther comprise evaluating one or more of: the suitability of thesubject for glycan treatment, the responsiveness of the subject toglycan treatment, and/or the progression of the glycan treatment in thesubject, comprising: a) acquiring a value for a parameter related to thelevel of a biomarker modulated by a glycan therapeutic preparation, andb) responsive to the value, classifying the subject, selecting atreatment for the subject, or administering the treatment to thesubject, thereby evaluating the subject. In one embodiment, one or morebiomarkers selected from: i) changes in gastrointestinal microbiota, ii)changes in metabolites of the gastric environment, iii) production oforganic acids, iv) modulation of the immune system, v) modulation ofinflammatory biomarkers, vi) modulation of immunoglobulins vii)increased absorption of minerals in the colon, viii) modulation of lipidmetabolism, ix) lowering of cholesterol, x) modulation of hosthomeostasis. In one embodiment, the modulation is of one or moremetabolic pathways listed in Table 19 ((super or sub pathways or levelof a metabolite). Provided herein is a method of treating symptomsassociated with gastrointestinal distress, comprising administering to asubject undergoing an anti-cancer therapy a glycan therapeuticcomposition comprising a mixture of branched glycans in an effectiveamount to treat one or more symptom associated with gastrointestinaldistress.

In one embodiment, the methods further comprise administering ananti-inflammatory agent. In one embodiment, the methods further compriseadministering a probiotic microorganism. In one embodiment, a beneficialgut bacterial microbiota is disturbed. In one embodiment, theanti-cancer therapy is radiation or chemotherapy. In one embodiment, thesymptom is constipation or diarrhea. In one embodiment, the symptom isgas, heartburn, stomach upset, bloating, flatulence, diarrhea, abdominalpain, cramping, nausea, or vomiting. In one embodiment, administrationof the composition results in a decrease in i) diarrhea, ii) a decreasein constipation, iii) a reduction in toxic catabolites. In oneembodiment, a reduction or elimination of symptoms persists aftertreatment of the condition has concluded. In one embodiment,administration of the composition results in an improvement of bowelregularity. In one embodiment, the reduction in the at least one of theone or more symptoms of the gastrointestinal disorder followingtreatment is about a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%,or 100% decrease in a subject reported severity of the at least one ofthe one or more symptoms of the gastrointestinal disorder. In oneembodiment, the reduction in at least one of the one or more symptoms ofthe gastrointestinal disorder persists for at least about a day, a week,a month, 3 months, 6 months, 9 months, or a year after treatment.

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the glycan therapeuticpreparation has an average degree of branching (DB) of at least 0.01,iv) at least 50% of the glycans in the preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, v) theratio of alpha- to beta-glycosidic bonds present in the glycans of thepreparation overall is between about 1:1 to about 5:1, or vi) anycombination of one, two, three, four or five of i), ii), iii), iv) andv).

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the branchedoligosaccharides comprise glucose, galactose, arabinose, mannose,fructose, xylose, fucose, or rhamnose glycan units, iv) the averagedegree of branching (DB) of the branched glycans in the glycantherapeutic preparation is between 0.01 and 0.3, v) at least 50% of theglycans in the glycan therapeutic preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, vi) theaverage DP of the glycan therapeutic preparation is between about DP6and about DP10, vii) the ratio of alpha- to beta-glycosidic bondspresent in the glycans of the glycan therapeutic preparation is betweenabout 1:1 to about 5:1, viii) the glycan therapeutic preparation has afinal solubility limit in water of at least about 60 Brix at 23° C., orix) any combination of one, two, three, or four, five, six, seven, oreight of i), ii), iii), iv), v), vi), vii), and viii).

For any and all of the foregoing methods, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise one or more glycan units, iii) the branched glycanscomprise at least 1% of branched glycan units, iv) the branched glycanshave a degree of polymerization (DP) of between 2 and 30 glycan units,v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- toalpha-configuration, vi) the branched glycans comprise a mixture of betaand alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3),and (2-6); vii) the glycan therapeutic preparation comprises a mixtureof branched glycans and unbranched glycans, viii) the glycan therapeuticpreparation comprises a mixture of digestible and non-digestibleglycans, or ix) any combination of one, two, three, or four, five, six,seven, or eight of i), ii), iii), iv), v), vi), vii), and viii).

For any and all of the foregoing aspects, and for any method describedherein that includes administering a glycan therapeutic preparation, theglycan therapeutic preparation may comprise one or more homo-glycansselected from xyl100, rha100, ara100, gal100, glu100, fuc100, fru100,and man100. For any method described herein that includes administeringa glycan therapeutic preparation, the glycan therapeutic preparation maycomprise one or more hetero-glycans selected from ara50gal50,xyl75gal25, ara80xyl20, ara60xyl40, ara50xyl50, glu80man20, glu60man40,man60glu40, man80glu20, gal75xyl25, glu50gal50, man62glu38, and thehybrid glycans glu90sor10 and glu90gly10. For any method describedherein that includes administering a glycan therapeutic preparation, theglycan therapeutic preparation may comprise one or more hetero-glycansselected from xyl75glu12gal12, xyl33glu33gal33, glu33gal33fuc33,man52glu29gal19, and glu33gal33neu33. For any method described hereinthat includes administering a glycan therapeutic preparation, the glycantherapeutic preparation may comprise one or more homo or hetero-glycansselected from xyl100, rha100, ara100, gal100, glu100, man100, fuc100,fru100, ara50gal50, xyl75gal25, ara80xyl20, ara60xyl40, ara50xyl50,glu80man20, glu60man40, man60glu40, man80glu20, gal75xyl25, glu50gal50,man62glu38, and the hybrid glycans glu90sor10 and glu90gly10,xyl75glu12gal12, xyl33glu33gal33, glu33gal33fuc33, man52glu29gal19, andglu33gal33neu33. For any method described herein that includesadministering a glycan therapeutic preparation, the glycan therapeuticpreparation may comprise one or more homo or hetero-glycans selectedfrom ara50gal50, glu33gal33fuc33, glu50gal50, gal100, glu100, xyl100,ara100, ara60xyl40, glu80man20, glu60man40, man52glu29gal19, man100. Forany method described herein that includes administering a glycantherapeutic preparation, the glycan therapeutic preparation may compriseone or more homo-glycans selected from man100, xyl100, or glu100. Forany method described herein that includes administering a glycantherapeutic preparation, the glycan therapeutic preparation may compriseman100. For any method described herein that includes administering aglycan therapeutic preparation, the glycan therapeutic preparation maycomprise xyl100. For any method described herein that includesadministering a glycan therapeutic preparation, the glycan therapeuticpreparation may comprise glu100. For any method described herein thatincludes administering a glycan therapeutic preparation, the glycantherapeutic preparation may comprise one or more hetero-glycans selectedfrom glu50gal50, glu80man20, glu33gal33fuc33, man52glu29gal19. For anymethod described herein that includes administering a glycan therapeuticpreparation, the glycan therapeutic preparation may comprise glu50gal50.For any method described herein that includes administering a glycantherapeutic preparation, the glycan therapeutic preparation may compriseglu80man20. For any method described herein that includes administeringa glycan therapeutic preparation, the glycan therapeutic preparation maycomprise glu33gal33fuc33. For any method described herein that includesadministering a glycan therapeutic preparation, the glycan therapeuticpreparation may comprise man52glu29gal19.

For any and all of the foregoing aspects, and for any method in whichbeneficial bacteria are modulated the beneficial bacteria includebacteria of the genus Akkermansia, Anaerofilum, Bacteroides, Blautia,Bifidobacterium, Butyrivibrio, Clostridium, Coprococcus, Dialister,Dorea, Fusobacterium, Eubacterium, Faecalibacterium, Lachnospira,Lactobacillus, Phascolarctobacterium, Peptococcus, Peptostreptococcus,Prevotella, Roseburia, Ruminococcus, and Streptococcus, and/or one ormore of the species Akkermansia municiphilia, minuta, Clostridiumcoccoides, Clostridium leptum, Clostridium scindens, Dialister invisus,Eubacterium rectal, Eubacterium eligens, Faecalibacterium prausnitzii,Streptococcus salivarius, and Streptococcus thermophilus, and the taxalisted in Tables 1, 3, and 4.

In a sixth aspect, the invention relates to kits for treating cancer.Provided herein is a kit for treating cancer in a human subject,comprising: a package comprising (i) a first pharmaceutical compositioncomprising a glycan therapeutic preparation, (ii) optionally, a secondanti-neoplastic or anti-cancer pharmaceutical composition, and (iii)instructions for using the first and/or the second pharmaceuticalcompositions for treating cancer in a human patient.

In one embodiment, the glycan therapeutic preparation: i) comprisesbranched glycans, ii) the branched glycans comprise branchedoligosaccharides, iii) the glycan therapeutic preparation has an averagedegree of branching (DB) of at least 0.01, iv) at least 50% of theglycans in the preparation have a degree of polymerization (DP) of atleast 3 and less than 30 glycan units, v) the ratio of alpha- tobeta-glycosidic bonds present in the glycans of the preparation overallis between about 1:1 to about 5:1, or vi) any combination of one, two,three, four or five of i), ii), iii), iv) and v).

In one embodiment, the glycan therapeutic preparation: i) comprisesbranched glycans, ii) the branched glycans comprise branchedoligosaccharides, iii) the branched oligosaccharides comprise glucose,galactose, arabinose, mannose, fructose, xylose, fucose, or rhamnoseglycan units, iv) the average degree of branching (DB) of the branchedglycans in the glycan therapeutic preparation is between 0.01 and 0.3,v) at least 50% of the glycans in the glycan therapeutic preparationhave a degree of polymerization (DP) of at least 3 and less than 30glycan units, vi) the average DP of the glycan therapeutic preparationis between about DP6 and about DP10, vii) the ratio of alpha- tobeta-glycosidic bonds present in the glycans of the glycan therapeuticpreparation is between about 1:1 to about 5:1, viii) the glycantherapeutic preparation has a final solubility limit in water of atleast about 60 Brix at 23° C., or ix) any combination of one, two,three, or four, five, six, seven, or eight of i), ii), iii), iv), v),vi), vii), and viii).

In one embodiment, the glycan therapeutic preparation: i) comprisesbranched glycans, ii) the branched glycans comprise one or more glycanunits, iii) the branched glycans comprise at least 1% of branched glycanunits, iv) the branched glycans have a degree of polymerization (DP) ofbetween 2 and 30 glycan units, v) the branched glycans have a 1:1, 1:2,1:3, 1:4, or 1:5 beta- to alpha-configuration, vi) the branched glycanscomprise a mixture of beta and alpha linkages of one or more of (1-2),(1-3), (1-4), (1-6), (2-3), and (2-6); vii) the glycan therapeuticpreparation comprises a mixture of branched glycans and unbranchedglycans, viii) the glycan therapeutic preparation comprises a mixture ofdigestible and non-digestible glycans, or ix) any combination of one,two, three, or four, five, six, seven, or eight of i), ii), iii), iv),v), vi), vii), and viii).

In a seventh aspect, the invention relates to dosage forms for thetreatment of a disease, disorder or condition. Provided herein is a unitdosage form effective to treat a disease, disorder, or pathologicalcondition comprising a glycan therapeutic preparation formulated fororal, enteral, rectal, intravenous, or intratumoral administration.

In one embodiment, the disease, disorder, or pathological condition iscancer. In one embodiment, the disease, disorder, or pathologicalcondition is a nutritional imbalance. In one embodiment, the disease,disorder, or pathological condition is an immune imbalance. In oneembodiment, the unit dosage form is formulated as a pharmaceuticalcomposition. In one embodiment, the unit dosage form is formulated as amedical food. In one embodiment, the unit dosage form is formulated as adietary supplement. In one embodiment, the dosage form is formulated fororal consumption by a subject. In one embodiment, the dosage form isformulated to dissolve in an aqueous solution and is orally administeredas a beverage, syrup, solution, or suspension. In one embodiment, thedosage form is formulated for enteral administration. In one embodiment,the administration is nasogastric, nasojejunal, oral gastric, or oraljejuna. In one embodiment, the dosage form is formulated for rectaladministration. In one embodiment, the administration is enema,suppository, or colonoscopy. In one embodiment, the dosage form isformulated as a delayed release or time controlled system. In oneembodiment, the dosage form is formulated to release the therapeuticglycan preparation in a specific region of the GI tract. In oneembodiment, the specific region of the GI tract comprises the stomach,small intestine, large intestine, or colon. In one embodiment, thecomposition modulates the abundance of a bacterial genus present in theGI tract. In one embodiment, the bacterial taxa is bifidobacteria,bacterioides, akkamensia. In one embodiment, the bacterial taxa isBifidobacteria, Bifidobacteriales, Bacteroidales, Clostridiales,Parabacteroides, and Akkermansia. In one embodiment, the bacterial taxais Blautia, Bifidobacterium, Roseburia, Coprococcus, Lachnospiraceae,Faecalibacterium, Parabacteroides, and Ruminococcaceae. In oneembodiment, the composition modulates the abundance of a bacterial genuspresent in one or both of the small intestine or large intestine. In oneembodiment, the composition modulates the abundance of a bacterial genuspredominant in the small intestine selected from the group of genusAchromobacter, Agrobacterium, Blautia, Burkholderia, Coprococcus,Cryocola, Enterococcus, Eubacterium, Holdemania, Lactococcus,Mycobacterium, Pseudoramibacter, Ralstonia, Sphingomonas, Streptococcus,and Turicibacter. In one embodiment, the composition modulates theabundance of a bacterial genus predominant in the large intestineselected from the group of genus Anaerotruncus, Akkermansia,Bacteroides, Bilophila, Butyricimonas, Odoribacter, Parabacteroides,Phascolarctobacterium, Prevotella, and Ruminococcus.

In one embodiment, the glycan therapeutic preparation: i) comprisesbranched glycans, ii) the branched glycans comprise branchedoligosaccharides, iii) the glycan therapeutic preparation has an averagedegree of branching (DB) of at least 0.01, iv) at least 50% of theglycans in the preparation have a degree of polymerization (DP) of atleast 3 and less than 30 glycan units, v) the ratio of alpha- tobeta-glycosidic bonds present in the glycans of the preparation overallis between about 1:1 to about 5:1, or vi) any combination of one, two,three, four or five of i), ii), iii), iv) and v).

In one embodiment, the glycan therapeutic preparation: i) comprisesbranched glycans, ii) the branched glycans comprise branchedoligosaccharides, iii) the branched oligosaccharides comprise glucose,galactose, arabinose, mannose, fructose, xylose, fucose, or rhamnoseglycan units, iv) the average degree of branching (DB) of the branchedglycans in the glycan therapeutic preparation is between 0.01 and 0.3,v) at least 50% of the glycans in the glycan therapeutic preparationhave a degree of polymerization (DP) of at least 3 and less than 30glycan units, vi) the average DP of the glycan therapeutic preparationis between about DP6 and about DP10, vii) the ratio of alpha- tobeta-glycosidic bonds present in the glycans of the glycan therapeuticpreparation is between about 1:1 to about 5:1, viii) the glycantherapeutic preparation has a final solubility limit in water of atleast about 60 Brix at 23° C., or ix) any combination of one, two,three, or four, five, six, seven, or eight of i), ii), iii), iv), v),vi), vii), and viii).

In one embodiment, the glycan therapeutic preparation: i) comprisesbranched glycans, ii) the branched glycans comprise one or more glycanunits, iii) the branched glycans comprise at least 1% of branched glycanunits, iv) the branched glycans have a degree of polymerization (DP) ofbetween 2 and 30 glycan units, v) the branched glycans have a 1:1, 1:2,1:3, 1:4, or 1:5 beta- to alpha-configuration, vi) the branched glycanscomprise a mixture of beta and alpha linkages of one or more of (1-2),(1-3), (1-4), (1-6), (2-3), and (2-6); vii) the glycan therapeuticpreparation comprises a mixture of branched glycans and unbranchedglycans, viii) the glycan therapeutic preparation comprises a mixture ofdigestible and non-digestible glycans, or ix) any combination of one,two, three, or four, five, six, seven, or eight of i), ii), iii), iv),v), vi), vii), and viii).

In an eights aspect, the invention relates to a composition comprisingglycan therapeutic preparations. Provided herein is a compositioncomprising: a) a digestible glycan therapeutic preparation and asubstantially non-digestible saccharide or dietary fiber, b) asubstantially non-digestible glycan therapeutic preparation and adigestible saccharide or dietary fiber, c) a substantiallynon-digestible glycan therapeutic preparation and a substantiallynon-digestible saccharide or dietary fiber, or d) a digestible glycantherapeutic preparation and a digestible saccharide or dietary fiber,and any one of (a), (b), (c), (d) optionally comprising a probioticbacterium.

In one embodiment, the composition is formulated as a pharmaceuticalcomposition. In one embodiment, the composition further comprises apharmaceutically acceptable excipient or carrier. In one embodiment, thecomposition is formulated as a medical food. In one embodiment, thecomposition is labeled a medical food. In one embodiment, thecomposition is formulated as a dietary supplement. In one embodiment,the composition is labeled a dietary supplement. In one embodiment, thecomposition further comprises an essential nutrient. In one embodiment,the composition is effective to treat an immune imbalance. In oneembodiment, the composition is effective to treat a nutritionalimbalance. In one embodiment, the composition is effective to treat acancer. In one embodiment, the glycan therapeutic preparation isselectively digested by gut microbiota constituents. In one embodiment,selective digestion results in modulation of the composition and/oractivity of the gut microbiota. In one embodiment, the growth of one ormore of Bacteroides, Blautia, Clostridium, Fusobacterium, Eubacterium,Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia,Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli,Christensenella minuta, and Christensenellaceae is selectivelystimulated. In one embodiment, the glycan therapeutic preparation issubstantially non-digestible by humans in the absence of specificbacteria in the gut, wherein the specific bacteria are capable ofutilizing the glycan therapeutic as a carbon source. In one embodiment,the glycan therapeutic is resistant to gastric acidity. In oneembodiment, the glycan therapeutic is resistant to hydrolysis by amammalian enzyme. In one embodiment, the mammalian enzyme is humanamylase. In one embodiment, the glycan therapeutic is resistant togastrointestinal absorption.

Provided herein is a composition for use in any of the methods describedherein.

Provided herein is a dosage form comprising the composition.

For any and all of the foregoing, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the glycan therapeuticpreparation has an average degree of branching (DB) of at least 0.01,iv) at least 50% of the glycans in the preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, v) theratio of alpha- to beta-glycosidic bonds present in the glycans of thepreparation overall is between about 1:1 to about 5:1, or vi) anycombination of one, two, three, four or five of i), ii), iii), iv) andv).

For any and all of the foregoing, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise branched oligosaccharides, iii) the branchedoligosaccharides comprise glucose, galactose, arabinose, mannose,fructose, xylose, fucose, or rhamnose glycan units, iv) the averagedegree of branching (DB) of the branched glycans in the glycantherapeutic preparation is between 0.01 and 0.3, v) at least 50% of theglycans in the glycan therapeutic preparation have a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units, vi) theaverage DP of the glycan therapeutic preparation is between about DP6and about DP10, vii) the ratio of alpha- to beta-glycosidic bondspresent in the glycans of the glycan therapeutic preparation is betweenabout 1:1 to about 5:1, viii) the glycan therapeutic preparation has afinal solubility limit in water of at least about 60 Brix at 23° C., orix) any combination of one, two, three, or four, five, six, seven, oreight of i), ii), iii), iv), v), vi), vii), and viii).

For any and all of the foregoing, in one embodiment, the glycantherapeutic preparation: i) comprises branched glycans, ii) the branchedglycans comprise one or more glycan units, iii) the branched glycanscomprise at least 1% of branched glycan units, iv) the branched glycanshave a degree of polymerization (DP) of between 2 and 30 glycan units,v) the branched glycans have a 1:1, 1:2, 1:3, 1:4, or 1:5 beta- toalpha-configuration, vi) the branched glycans comprise a mixture of betaand alpha linkages of one or more of (1-2), (1-3), (1-4), (1-6), (2-3),and (2-6); vii) the glycan therapeutic preparation comprises a mixtureof branched glycans and unbranched glycans, viii) the glycan therapeuticpreparation comprises a mixture of digestible and non-digestibleglycans, or ix) any combination of one, two, three, or four, five, six,seven, or eight of i), ii), iii), iv), v), vi), vii), and viii).

For any and all of the foregoing aspects, and for any pharmaceuticalcomposition, medical food, dietary supplement, dosage form, or kitcomprising a glycan therapeutic preparation described herein, the glycantherapeutic preparation may comprise one or more homo-glycans selectedfrom xyl100, rha100, ara100, gal100, glu100, fuc100, fru100, and man100.For any pharmaceutical composition, medical food, dietary supplement,dosage form, or kit comprising a glycan therapeutic preparationdescribed herein, the glycan therapeutic preparation may comprise one ormore hetero-glycans selected from ara50gal50, xyl75gal25, ara80xyl20,ara60xyl40, ara50xyl50, glu80man20, glu60man40, man60glu40, man80glu20,gal75xyl25, glu50gal50, man62glu38, and the hybrid glycans glu90sor10and glu90gly10. For any pharmaceutical composition, medical food,dietary supplement, dosage form, or kit comprising a glycan therapeuticpreparation described herein, the glycan therapeutic preparation maycomprise one or more hetero-glycans selected from xyl75glu12gal12,xyl33glu33gal33, glu33gal33fuc33, man52glu29gal19, and glu33gal33neu33.For any pharmaceutical composition, medical food, dietary supplement,dosage form, or kit comprising a glycan therapeutic preparationdescribed herein, the glycan therapeutic preparation may comprise one ormore homo or hetero-glycans selected from xyl100, rha100, ara100,gal100, glu100, man100, fuc100, fru100, ara50gal50, xyl75gal25,ara80xyl20, ara60xyl40, ara50xyl50, glu80man20, glu60man40, man60glu40,man80glu20, gal75xyl25, glu50gal50, man62glu38, and the hybrid glycansglu90sor10 and glu90gly10, xyl75glu12gal12, xyl33glu33gal33,glu33gal33fuc33, man52glu29gal19, and glu33gal33neu33. For anypharmaceutical composition, medical food, dietary supplement, dosageform, or kit comprising a glycan therapeutic preparation describedherein, the glycan therapeutic preparation may comprise one or more homoor hetero-glycans selected from ara50gal50, glu33gal33fuc33, glu50gal50,gal100, glu100, xyl100, ara100, ara60xyl40, glu80man20, glu60man40,man52glu29gal19, man100. For any pharmaceutical composition, medicalfood, dietary supplement, dosage form, or kit comprising a glycantherapeutic preparation described herein, the glycan therapeuticpreparation may comprise one or more homo-glycans selected from man100,xyl100, or glu100. For any pharmaceutical composition, medical food,dietary supplement, dosage form, or kit comprising a glycan therapeuticpreparation described herein, the glycan therapeutic preparation maycomprise man100. For any pharmaceutical composition, medical food,dietary supplement, dosage form, or kit comprising a glycan therapeuticpreparation described herein, the glycan therapeutic preparation maycomprise xyl100. For any pharmaceutical composition, medical food,dietary supplement, dosage form, or kit comprising a glycan therapeuticpreparation described herein, the glycan therapeutic preparation maycomprise glu100. For any pharmaceutical composition, medical food,dietary supplement, dosage form, or kit comprising a glycan therapeuticpreparation described herein, the glycan therapeutic preparation maycomprise one or more hetero-glycans selected from glu50gal50,glu80man20, glu33gal33fuc33, man52glu29gal19. For any pharmaceuticalcomposition, medical food, dietary supplement, dosage form, or kitcomprising a glycan therapeutic preparation described herein, the glycantherapeutic preparation may comprise glu50gal50. For any pharmaceuticalcomposition, medical food, dietary supplement, dosage form, or kitcomprising a glycan therapeutic preparation described herein, the glycantherapeutic preparation may comprise glu80man20. For any pharmaceuticalcomposition, medical food, dietary supplement, dosage form, or kitcomprising a glycan therapeutic preparation described herein, the glycantherapeutic preparation may comprise glu33gal33fuc33. For anypharmaceutical composition, medical food, dietary supplement, dosageform, or kit comprising a glycan therapeutic preparation describedherein, the glycan therapeutic preparation may comprise man52glu29gal19.

For any and all of the foregoing aspects, and for any pharmaceuticalcomposition, medical food, dietary supplement, dosage form, or kitcomprising a probiotic bacteria, and any method that includesadministering a probiotic bacteria, the a probiotic bacteria maycomprise bacteria of the genus Akkermansia, Anaerofilum, Bacteroides,Blautia, Bifidobacterium, Butyrivibrio, Clostridium, Coprococcus,Dialister, Dorea, Fusobacterium, Eubacterium, Faecalibacterium,Lachnospira, Lactobacillus, Phascolarctobacterium, Peptococcus,Peptostreptococcus, Prevotella, Roseburia, Ruminococcus, andStreptococcus, and/or one or more of the species Akkermansiamuniciphilia, minuta, Clostridium coccoides, Clostridium leptum,Clostridium scindens, Dialister invisus, Eubacterium rectal, Eubacteriumeligens, Faecalibacterium prausnitzii, Streptococcus salivarius, andStreptococcus thermophilus, and the taxa listed in Tables 1, 3, and 4.

For any and all of the foregoing aspects, and for any pharmaceuticalcomposition, medical food, dietary supplement, dosage form, or kitcomprising an anti-cancer agent or drug, and any method that includesadministering a cancer agent, the cancer agent may comprise, e.g.,checkpoint inhibitors (such as, e.g., anti-PD-1, anti-PD-L1, anti-CTLA4,anti-TIM-3, anti-LAG-3); vaccines (such as, e.g., autologous cancervaccines, allogeneic cancer vaccines, neoantigen cancer vaccines, sharedantigen cancer vaccines (e.g. NY-ESO-1)); targeted kinase inhibitors(such as, e.g., Imatinib mesylate, Ibrutinib, Neratinib, Palpociclib,Erlotinib, Lapatinib); antibodies (such as, e.g., Bevacizumab,Trastuzumab, Rituximab, Cetuximab); chemotherapeutics (such as, e.g.,irinotecan, 5-flurouracil, lenalidomide, capecitabine, docetaxel),antibody-drug conjugates (e.g. ado-trastuzumab emtansine), and any otheranti-cancer drug mentioned elsewhere herein. In one embodiment, theanti-cancer agent is PD-L1. In one embodiment, the anti-cancer is 5-FUand/or irinotecan.

For any and all of the foregoing aspects, and for any pharmaceuticalcomposition, medical food, dietary supplement, dosage form, or kitcomprising an immunomodulatory agent or drug (e.g., pro- oranti-inflammatory), and any method that includes administering animmunomodulatory agent (e.g., pro- or anti-inflammatory), theimmunomodulatory agent may comprise, e.g., pro-inflammatory agents (e.g.pro-inflammatory cytokines), anti-inflammatory agents (e.g.anti-inflammatory cytokines, NSAIDs, anti-allergy agents), steroids,hormones, interleukins, vaccines/antigens, anti-microbial agents (e.g.anti-virals) and anti-neoplastic agents.

For any and all of the foregoing aspects, and for any pharmaceuticalcomposition, medical food, dietary supplement, dosage form, or kitcomprising a metabolism modulating agent or drug, and any method thatincludes administering an metabolism modulating agent, the metabolismmodulating agent may comprise, e.g., insulin, metformin, lorcaserin,somatropin, miglitol, sitagliptin, simvastatin, progestagens,corticosteroids, hormones, and interleukins.

In any and all of the foregoing aspects, in some embodiments, theinvention features compounds and compositions (e.g., pharmaceuticalcompositions, medical foods, or dietary supplements) for use in, e.g.,treating an immune imbalance in a subject; reducing an infection and/oran inflammation in a subject having an immune imbalance; modulating thecomposition and/or metabolic activity of the intestinal bacterialcommunity of a subject having an immune imbalance; treating a dysbiosisin a subject having an immune imbalance; treating a nutritionalimbalance in a subject; modulating the composition and/or metabolicactivity of the intestinal bacterial community of a subject having anutritional imbalance; treating a dysbiosis in a subject having anutritional imbalance; treating cancer in a subject; modulating thecomposition and/or metabolic activity of the intestinal bacterialcommunity of a subject having cancer; treating a dysbiosis in a subjecthaving cancer; reducing an infection and/or an inflammation in a subjecthaving cancer; inducing apoptosis of a cancer or a precancerous cell ina subject having cancer; reducing the risk of cancer in a subject;modulating the composition of the intestinal bacterial community of asubject having cancer; modulating the metabolic activity of theintestinal bacterial community of a subject having cancer; reducing asymptom of a treatment or therapy in a subject; reducing toxicity of adrug treatment or therapy in a subject; treating symptoms associatedwith gastrointestinal distress; modulating the function and/or activityof a pathway of a subject having an immune imbalance; modulating thefunction and/or activity of a pathway of a subject having a nutritionalimbalance; and/or modulating the function and/or activity of a pathwayof a subject having cancer.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 : A representative SEC curve between 16 and 20.5 minutes of aglu100 sample showing the average MW and the MW at 10% of maximumabsorption on both the leading and trailing edges of the curve.

FIG. 2 : A representative anomeric region of an ¹H-¹³C HSQC spectrum ofa glu100 sample showing the signal distribution of alpha- andbeta-glycosidic bonds

FIGS. 3A-3C. A representative anomeric region of an ¹H-¹³C HSQC spectrumof glu100 (FIG. 3A), glu50gal50 (FIG. 3B), and gal100 (FIG. 3C) samples,demonstrating the additive effect of the fingerprint peaks.

FIG. 4 : Representative GC chromatograms of three representativepermethylated and hydrolyzed glycans showing distribution ofregiochemistry as assigned by comparison to known standards.

FIG. 5 . A representative partial assignment of the peaks in theanomeric region of a glu100 sample ¹H-¹³C HSQC spectrum showing theseparation between alpha and beta isomers in the ¹H axis, with alphaisomers downfield (¹H>4.8 ppm in this case) and beta isomers upfield(¹H<4.8 ppm in this case). In addition, terminal and internal sugars canbe distinguished in the ¹³C axis with terminal sugars upfield (¹³C<94ppm for alpha and ¹³C<100 ppm for beta in this case) and internal sugarsdownfield (¹³C>94 ppm for alpha and ¹³C>100 ppm for beta in this case).

FIGS. 6A-6B. A portion of an exemplary catalyst with a polymericbackbone and side chains is illustrated in FIG. 6A. A portion of anexemplary catalyst, in which a side chain with the acidic group isconnected to the polymeric backbone by a linker and in which a sidechain with the cationic group is connected directly to the polymericbackbone is illustrated in FIG. 6B.

FIG. 7A. Anomeric region of the 1H-13C HSQC spectrum of man100. FIG. 7B.Anomeric region of the 1H-13C HSQC spectrum of xyl100.

FIGS. 8A-8E. Taxa shifts in human fecal slurry grown with selectedglycan therapeutics. FIG. 8A: Bacterial phyla, percent (%) relativeabundance in 1% fecal slurry exposed to no added carbon, xyl100,man52glu29gal19, glu100, and FOS; FIG. 8B: Bifidobacteriales % relativeabundance in 1% fecal slurry exposed to no added carbon, xyl100,man52glu29gal19, glu100, and FOS; FIG. 8C: Bifidobacteria % relativeabundance in 1% fecal slurry exposed to no added carbon, xyl100,man52glu29gal19, glu100, and FOS; FIG. 8D: Bacteroidales % relativeabundance in 1% fecal slurry exposed to no added carbon, xyl100,man52glu29gal19, glu100, and FOS; FIG. 8E: Clostridiales % relativeabundance in 1% fecal slurry exposed to no added carbon, xyl100,man52glu29gal19, glu100, and FOS.

FIG. 9 . Relative abundance of OTU 51 in individuals treated withglu50gal50. Dashed vertical lines represent treatment doses. 62% ofindividuals did not have this OTU in their gut microbiota prior totreatment.

FIG. 10 . Distances were calculated for each mouse between microbiotasampled at 1 day before and 5 days after glycan or water administrated.The larger the distance, the bigger change in microbial composition isobserved.

FIG. 11 . Shannon diversity index. Paired Wilcoxon test was used tocalculate the significance of observed differences.

FIGS. 12A-12B. Relative abundance of sequences assigned to genusAkkermansia, phylum Verrucomicrobia is shown in FIG. 12A Relativeabundance of sequences assigned to genus Blautia, phylum Firmicutes isshown in FIG. 12B.

FIG. 13 . SCFA concentrations in supernatants of BUN.80 and DLO.76 grownwith either FOS or glycan glu80man20

FIG. 14 . Most abundant SCFA in the cecal contents of mice fed either anormal mouse chow, high fat diet, or high fat diet+glycans.(*P<0.05,**P<0.01, Wilcox, FDR corrected).

FIG. 15 . PCoA of metabolomic profile.

FIG. 16 . PCoA of bile acid composition of mouse cecal contents onNormal Chow and High Fat Diet+/−glycan treatment.

FIG. 17 . Glycan treatment resulting in a reduction of (A) DCA(deoxycholic acid) and (B) LCA (lithocholic acid) compared to high fatcontrol.

FIG. 18 . White blood cell count on Day 5; bars represent mean andstandard deviation. Significance was determined by using one-way ANOVAwith Dunnett's multiple comparisons test. *p<0.05.

FIG. 19 . Effect of commercial fibers and novel glycans on colonicpropulsion in morphine-treated mice. Significance was determined byusing one-way ANOVA with Dunnett's multiple comparisons test. *p<0.05,**p<0.01.

FIGS. 20A-20B. Colonic propulsion in treatment responder (FIG. 20A) andtreatment non-responder (FIG. 20B) groups. Average time to beadexpulsion, an indicator of colonic propulsion, was similar in animalsthat responded to naloxone, xyl100 and XOS. Likewise, average time tobead expulsion in responders was similar in PDX and ara100. Time to beadexpulsion was similar across all non-responder groups regardless oftreatment.

FIG. 21 . Tumor growth curves: Group 1 received vehicle treatment (graylong-dashed line), Group 2 mice received man100 (black solid line),Group 3 mice received anti-PD-L1 (gray shortest-dashed line), and Group4 mice received the bifidobacteria mix (gray medium-dashed line). Basedon one-way ANOVA, the difference between Group 1 and Group 2 wassignificant with a p<0.05 on days 21, 24, 28, and 31. Values shown aremean+/−standard deviation across the groups.

FIG. 22 . Spider plots of vehicle control (Group 1, thin gray dottedlines), anti-PD-L1 (Group 3, thick gray solid lines), and man100 (Group2, thick black solid lines) show tumor growth curves for each mouse fromdays 7-31.

DETAILED DESCRIPTION OF THE INVENTION

Described herein are preparations of glycan therapeutics andpharmaceutical compositions, medical foods and dietary supplementsthereof, and related methods, which have been found to be effective totreat a number of diseases, disorders or pathological conditions.

Definitions

As used herein, the term “abundance” as it relates to a microbial taxarefers to the presence of one microbial taxa as compared to anothermicrobial taxa in a defined microbial niche, such as the GI tract, or inthe entire host organism (e.g. a human or a laboratory animal model ofdisease).

“Acquire” or “acquiring” as the terms are used herein, refer toobtaining possession of a value, e.g., a numerical value, or image, or aphysical entity (e.g., a sample), by “directly acquiring” or “indirectlyacquiring” the value or physical entity. “Directly acquiring” meansperforming a process (e.g., performing a synthetic or analytical methodor protocol) to obtain the value or physical entity. “Indirectlyacquiring” refers to receiving the value or physical entity from anotherparty or source (e.g., a third party laboratory that directly acquiredthe physical entity or value). Directly acquiring a value or physicalentity includes performing a process that includes a physical change ina physical substance or the use of a machine or device. Examples ofdirectly acquiring a value include obtaining a sample from a humansubject. Directly acquiring a value includes performing a process thatuses a machine or device, e.g., an NMR spectrometer to obtain an NMRspectrum.

As used herein, “antibody” is used in the broadest sense and includesmonoclonal antibodies (including full length or intact monoclonalantibodies), polyclonal antibodies, multivalent antibodies,multispecific antibodies (e.g., bispecific antibodies), and antibodyfragments so long as they exhibit the desired activity.

As used herein, the term “cancer” refers to a cell (or cells) that hasan aberrant capacity for autonomous growth or replication and anabnormal state or condition (e.g. of a tissue or organ) characterized byproliferative cell growth. “Cancer” as used herein includes any solid orliquid, benign or malignant, non-invasive or invasive cancer or tumor,including hyperplasias, neoplasms, carcinoma, sarcoma, or ahematopoietic neoplastic disorder (e.g., a leukemia) and pre-cancerousor premalignant lesions.

As used herein, “colonization” of a host organism refers to thenon-transitory residence of a bacterium or other microbial organism in aniche.

As used herein, a “combination therapy” or “administered in combination”means that two (or more) different agents or treatments are administeredto a subject as part of a defined treatment regimen for a particulardisease or condition. The treatment regimen defines the doses andperiodicity of administration of each agent such that the effects of theseparate agents on the subject overlap. In some embodiments, thedelivery of the two or more agents is simultaneous or concurrent and theagents may be co-formulated. In other embodiments, the two or moreagents are not co-formulated and are administered in a sequential manneras part of a prescribed regimen. In some embodiments, administration oftwo or more agents or treatments in combination is such that thereduction in a symptom, or other parameter related to the disorder isgreater than what would be observed with one agent or treatmentdelivered alone or in the absence of the other. The effect of the twotreatments can be partially additive, wholly additive, or greater thanadditive (e.g., synergistic). Sequential or substantially simultaneousadministration of each therapeutic agent can be effected by anyappropriate route including oral routes, intravenous routes,intramuscular routes, and direct absorption through mucous membranetissues. The therapeutic agents can be administered by the same route orby different routes. For example, a first therapeutic agent of thecombination may be administered by intravenous injection while a secondtherapeutic agent of the combination may be administered orally.

“Diversity of a microbial community” or “microbial diversity” as usedherein refers to the diversity found in the microbiota of a within agiven niche or host subject. Diversity can relate to the number ofdistinct microbial taxa and/or richness of the microbial taxa within theniche or host and can be expressed, e.g. using the Shannon Diversityindex (Shannon entropy), alpha-beta diversity, total number of observedOTUs, or Chao1 index, as described herein. In some embodiments, amicrobiome regulator described herein modulates diversity within amicrobial community, which may be expressed using Shannon entropy as ameasure. For example, the more unequal the abundances of the bacterialtaxa, the larger the weighted geometric mean of the p_(i) values inShannon's formula, and the smaller the corresponding Shannon entropy. Ifpractically all abundance is concentrated to one taxa, and the othertaxa are very rare (even if there are many of them), Shannon entropyapproaches zero. When there is only one taxa Shannon entropy exactlyequals zero.

As used herein, a “dosage regimen”, “dosing regimen”, or “treatmentregimen” is a modality of drug administration that achieves atherapeutic objective. A dosage regimen includes definition of one, two,three, or four of: a route of administration, a unit dose, a frequencyof dosage, or a length of treatment.

As used herein, a “dysbiosis” refers to the state of the microbiotaunder conditions of host disease, predisposition to host disease, orother unwanted condition or symptom of the host. In an embodiment,dysbiosis refers to the state of the microbiota under conditions ofdisease. Dysbiosis can be contrasted with eubiosis, which refers to thestate of the microbiota under healthy conditions of the host. The stateof the microbiota may include the characteristics relating to either thestructure or function of the microbiota. In an embodiment, a dysbiosisincludes an imbalance in the state of the microbiota, wherein the normaldiversity or relative abundance of a microbial taxa is affected, e.g.,relative to a second bacterial taxa or relative to the abundance of saidtaxa under conditions of health. In an embodiment, a dysbiosis comprisesan imbalance in the function of the microbiota, e.g., a change in levelof gene expression, level of a gene product, or metabolic output (e.g.,an immune function such as immune surveillance it the inflammationresponse). In some embodiments, a dysbiosis is an undesired, e.g.,unhealthy, state associated with unwanted symptoms in the host and thatno longer promotes health.

A “dysbiosis of the gastrointestinal microbiota” refers to an imbalancedstate of the microbiota of the GI tract (e.g., in the stomach, smallintestine, or large intestine).

As used herein, “ecological niche” or simply “niche” refers to theecological space in which an organism or group of organisms occupies(such as the GI tract or one or more subsection of the GI-tract, suchas, e.g., the stomach, the large and small intestine, the rectum, etc.).In some embodiments, niche specifically refers to a space thatmicroorganisms occupy. Niche may describe how an organism or populationof organisms responds to the distribution of resources, physicalparameters (e.g., host tissue space) and competitors (e.g., by growingwhen resources are abundant, and when predators, parasites and pathogensare scarce) and how it in turn alters those same factors (e.g., limitingaccess to resources by other organisms, acting as a food source forpredators and a consumer of prey).

An “effective amount” and “therapeutically effective amount” as usedherein refers to an amount of a pharmaceutical composition or a drugagent that is sufficient to provide a desired effect. In someembodiments, a physician or other health professional decides theappropriate amount and dosage regimen. An effective amount also refersto an amount of a pharmaceutical composition or a drug agent thatprevents the development or relapse of a medical condition.

As used herein, a “glycan therapeutic preparation” (also referred to asa “preparation of glycan therapeutics”, “glycan preparation” or “glycantherapeutic”) is a preparation comprising glycans (sometimes referred toas glycan species) that exhibits a therapeutic effect. A glycantherapeutic comprises a synthetic mixture of a plurality of mono-, di-,oligomeric and/or polymeric glycan species (e.g. oligo- and/orpolysaccharides, referred to as “oligosaccharides”), wherein theoligomeric and/or polymeric glycan species comprise glycan units thatare linked by glycosidic bonds. In some embodiments, a glycantherapeutic may be formulated into a pharmaceutical composition, amedical food or dietary supplement for human use. In some embodiments, aglycan therapeutic may be formulated in any suitable dosage formincluding a kit. In some embodiments, preparations of glycantherapeutics do not contain one or more naturally occurring oligo- orpolysaccharide, including: glucooligosaccharide, mannanoligosaccharide,inulin, lychnose, maltotretraose, nigerotetraose, nystose, sesemose,stachyose, isomaltotriose, nigerotriose, maltotriose, melezitose,maltotriulose, raffinose, kestose, fructooligosaccharide,2′-fucosyllactose, galactooligosaccharide, glycosyl, idraparinux,isomaltooligosaccharide, maltodextrin, xylooligosaccharide, agar,agarose, alginic acid, alguronic acid, alpha glucan, amylopectin,amylose, arabioxylan, beta-glucan, callose, capsulan, carrageenan,cellodextrin, cellulin, cellulose, chitin, chitin nanofibril,chitin-glucan complex, chitosan, chrysolaminarin, curdlan, cyclodextrin,alpha-cylcodextrin, dextran, dextrin, dialdehyde starch, ficoll,fructan, fucoidan, galactoglucomannan, galactomannan,galactosamineogalactan, gellan gum, glucan, glucomannan,glucoronoxyland, glycocalyx, glycogen, hemicellulose, hypromellose,icodextrin, kefiran, laminarin, lentinan, levan polysaccharide,lichenin, mannan, mucilage, natural gum, paramylon, pectic acid, pectin,pentastarch, phytoglycogen, pleuran, poligeenan, polydextrose,porphyran, pullulan, schizophyllan, sepharose, sinistrin, sizofiran,sugammadex, welan gum, xantham gum, xylan, xyloglucan, zymosan, and thelike. In some embodiments, a glycan exists as a salt, e.g., apharmaceutically acceptable salt.

A “glycan unit” as used herein refers to the individual unit of a glycanspecies disclosed herein, e.g., the building blocks from which theglycan species is made. In an embodiment, a glycan unit is a monomer. Inan embodiment, a glycan unit is a dimer. In an embodiment a glycan unitis a monosaccharide. In an embodiment, a glycan unit is a disaccharide.In some embodiments, the glycan unit is a carbohydrate and may beselected from a sugar alcohol, a short-chain fatty acid, a sugar acid,an imino sugar, a deoxy sugar, and an amino sugar. In some embodiments,the glycan unit is erythrose, threose, erythulose, arabinose, lyxose,ribose, xylose, ribulose, xylulose, allose, altrose, galactose, glucose,gulose, idose, mannose, talose, fructose, psicose, sorbose, tagatose,fucose, fuculose, rhamnose, mannoheptulose, sedoheptulose, and the like.In some embodiments, the glycan unit is glucose, galactose, arabinose,mannose, fructose, xylose, fucose, or rhamnose. In embodiments, a glycancomprises distinct glycan units, e.g., a first and a secondmonosaccharide, or a first and a second disaccharide, or a monosaccarideand a disaccharide. In embodiments, a glycan comprises distinct glycanunits, e.g., a first, a second, a third, a fourth, and/or a fifthdistinct glycan unit.

As used herein, an “isolated” or “purified” glycan therapeuticpreparation (also sometimes referred to as “polished”) is substantiallypure and free of contaminants, e.g. pathogens or otherwise unwantedbiological material, or toxic or otherwise unwanted organic or inorganiccompounds. In some embodiments, pure or isolated compounds, compositionsor preparations may contain traces of solvents and/or salts (such asless than 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, less than 0.5% or0.1% by w/w, w/v, v/v or molar %). Purified compounds are orpreparations contain at least about 60% (by w/w, w/v, v/v or molar %),at least about 75%, at least about 90%, at least about 95%, at leastabout 97%, at least about 98%, or at least about 99% by w/w, w/v, v/v ormolar % the compound(s) of interest. For example, a purified(substantially pure) or isolated preparation of glycan therapeutics isone that is at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 98%, 99%,99.5%, 99.8%, 99.9% or 100% of the glycan therapeutic by w/w, w/v, v/vor molar % (i.e. not including any solvent, such as e.g. water, in whichthe glycan therapeutic preparation may be dissolved) and separated fromthe components that accompany it, e.g. during manufacture,extraction/purification and/or processing (e.g. such that the glycantherapeutic is substantially free from undesired compounds). Purity maybe measured by any appropriate standard method, for example, by columnchromatography (e.g., size-exclusion chromatography (SEC)), thin layerchromatography (TLC), gas chromatography (GC), high-performance liquidchromatography (HPLC) or nuclear magnatic resonance (NMR) spectroscopy.Purified or purity may also define a degree of sterility that is safefor administration to a human subject, e.g., lacking viable infectiousor toxic agents.

As used herein, “microbiome” refers to the genetic content of thecommunities of microbes that live in and on a subject (e.g. a humansubject), both sustainably and transiently, including eukaryotes,archaea, bacteria, and viruses (including bacterial viruses (e.g.,phage)), wherein “genetic content” includes genomic DNA, RNA such asribosomal RNA and messenger RNA, the epigenome, plasmids, and all othertypes of genetic information. In some embodiments, microbiomespecifically refers to genetic content of the communities ofmicroorganisms in a niche.

“Microbiota” as used herein refers to the community of microorganismsthat occur (sustainably or transiently) in and on a subject (e.g. ahuman subject), including eukaryotes, archaea, bacteria, and viruses(including bacterial viruses, e.g. phage). In some embodiments,microbiota specifically refers to the microbial community in a niche.

“Modulate the microbiota” or “modulating the microbiota” as used hereinrefers to changing the state of the microbiota. Changing the state ofthe microbiota may include changing the structure and/or function of themicrobiota. A change in the structure of the microbiota is, e.g., achange in the relative composition of a taxa, e.g., in one or moreregion of the GI tract such as the cecum, ascending colon, transversecolon, descending colon, sigmoid colon, and/or rectum. In an embodiment,a change in the structure of the microbiota comprises a change in theabundance of a taxa, e.g., relative to another taxa or relative to whatwould be observed in the absence of the modulation. Modulation of themicrobiota may also, or in addition, include a change in a function ofthe microbiota, such as a change in microbiota gene expression, level ofa gene product (e.g., RNA or protein), or metabolic output of themicrobiota. Functions of the microbiota may also include host pathogenprotection, host nutrition, host metabolism and host immune modulation.Modulation of the structure or function of the microbiota mayadditionally induce a change in one or more functional pathway of thehost (e.g., a change in gene expression, level of a gene product, and/ormetabolic output of a host cell or host process) as a result of a changein the microbiota or its function.

As used herein, the term “oligosaccharide” refers to a moleculeconsisting of multiple (i.e., two or more) individual glycan unitslinked covalently. Each glycan unit may be linked through a glycosidicbond (e.g., a 1 →2 glycosidic bond, a 1 →3 glycosidic bond, a 1 →4glycosidic bond, a 1 →5 glycosidic bond or a 1 →6 glycosidic bond)present in either the alpha or beta configuration. As used herein, theterm “pathogenic” (e.g. “pathogenic bacteria”) refers to a substance,microorganism or condition that has the capability to cause a disease.In certain contexts, pathogens also include microbes (e.g. bacteria)that are associated with a disease or condition but for which acausative relationship (e.g., a direct causative relationship) has notbeen established or has yet to be established.

As used herein, a “pharmaceutical composition” or “pharmaceuticalpreparation” is a composition or preparation having pharmacologicalactivity or other direct effect in the mitigation, treatment, orprevention of disease, and/or a finished dosage form or formulationthereof and is for human use. A pharmaceutical composition orpharmaceutical preparation is typically produced under goodmanufacturing practices (GMP) conditions. Pharmaceutical compositions orpreparations may be sterile or non-sterile. If non-sterile, suchpharmaceutical compositions meet the microbiological specifications andcriteria for non-sterile pharmaceutical products as described in theU.S. Pharmacopeia (USP) or European Pharmacopoeia (EP). Pharmaceuticalcompositions may further comprise or may be co-administered withadditional active agents, such as, e.g. additional therapeutic agents.Pharmaceutical compositions may also comprise pharmaceuticallyacceptable excipients, solvents, carriers, fillers, or any combinationthereof.

The term “phenotype” refers to a set of observable characteristics of anindividual entity. For example, an individual subject may have aphenotype of “healthy” or “diseased.” A phenotype may describe the stateof an entity, wherein all entities within a phenotype share the same setof characteristics that describe the phenotype. The phenotype of anindividual results in part, or in whole, from the interaction of theentities genome and/or microbiome with the environment. As used herein,the term “polysaccharide” refers to a polymeric molecule consisting ofmultiple individual glycan units linked covalently. In some embodiments,a polysaccharide comprises at least 10 or more glycan units (e.g., atleast 10, at least 15, at least 20, at least 25, or at least 50, atleast 100, at least 250, at least 500, or at least 1000 glycan units).Each glycan unit may be linked through a glycosidic bond (e.g., a 1 →2glycosidic bond, a 1 →3 glycosidic bond, a 1 →4 glycosidic bond, a 1 →5glycosidic bond and a 1 →6 glycosidic bond) present in either the alphaor beta configuration. In some embodiments, a polysaccharide is ahomogenous polymer comprising identical repeating units. In otherembodiments, a polysaccharide is a heterogenous polymer comprised ofvaried repeating units. Polysaccharides may further be characterized bya degree of branching (DB, branching points per residue) or a degree ofpolymerization (DP). As used herein, the term “subject” or “patient”generally refers to any human subject. The term does not denote aparticular age or gender. Subjects may include pregnant women. Subjectsmay include a newborn (a preterm newborn, a full term newborn), aninfant up to one year of age, young children (e.g., 1 yr to 12 yrs),teenagers, (e.g., 13-19 yrs), adults (e.g., 20-64 yrs), and elderlyadults (65 yrs and older). A subject does not include an agriculturalanimal, e.g., farm animals or livestock, e.g., cattle, horses, sheep,swine, chickens, etc. In general, a subject comprises a host and itscorresponding microbiota.

A “substantial decrease” as used herein is a decrease of 5%, 10%, 20%,30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.9%, or 100%.

A “substantial increase” as used herein is an increase of 10%, 20%, 30%,40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 250%, 300%, 350%, 400%,450%, 500%, 550%, 600%, 650%, 700%, 750%, 800%, 850%, 900%, 950%, 1000%,or more than 1000%.

“Synthetic” as used herein refers to a man-made compound or preparation,such as a glycan therapeutic preparation, that is not naturallyoccurring. In one embodiment, the polymeric catalyst described herein isused to synthesize the glycans of the preparation under suitablereaction conditions, e.g. by a polymerization reaction that createsoligomers and polymers from individual glycan units that are added tothe reaction. In some embodiments, the polymeric catalyst acts as ahydrolysis agent and can break glycosidic bonds. In other embodiments,the polymer catalyst can form glycosidic bonds. Synthetic glycantherapeutic preparations may also include glycan therapeutics that arenot isolated from a natural oligo- or polysaccharide source. It is to beunderstood that while the glycan therapeutic preparation is not isolatedfrom a natural oligo- or polysaccharide source, the glycan units makingup the glycan therapeutic can be and often are isolated from naturaloligo- or polysaccharide sources, including those listed herein, or aresynthesized de novo.

The terms “treating” and “treatment” as used herein refer to theadministration of an agent or composition to a subject (e.g., asymptomatic subject afflicted with an adverse condition, disorder, ordisease) so as to affect a reduction in severity and/or frequency of asymptom, eliminate a symptom and/or its underlying cause, and/orfacilitate improvement or remediation of damage, and/or preventing anadverse condition, disorder, or disease in an asymptomatic subject whois susceptible to a particular adverse condition, disorder, or disease,or who is suspected of developing or at risk of developing thecondition, disorder, or disease.

Generation of Glycan Therapeutic Preparations

Preparations comprising a plurality of glycans such as, e.g.,oligosaccharide mixtures can be generated using a non-enzymaticcatalyst, e.g., the polymeric catalyst described in U.S. Pat. No.8,466,242, “POLYMERIC ACID CATALYSTS AND USES THEREOF” or by othersuitable methods. Methods to prepare the polymeric and solid-supportedcatalysts described herein can be found in WO 2014/031956, “POLYMERICAND SOLID-SUPPORTED CATALYSTS, AND METHODS OF DIGESTING CELLULOSICMATERIALS USING SUCH CATALYSTS.” The glycans generated, e.g., by usingthe catalyst, for example as described in WO 2016/007778,“OLIGOSACCHARIDE COMPOSITIONS AND METHODS FOR PRODUCING THEREOF” can bestructurally much more diverse glycans than those produced by enzymaticreactions. All patent applications are incorporated herein by reference.Provided are also methods for generating the preparations of glycans(e.g. oligosaccharides) described herein, for example by: a) providingone or more mono- or disaccharide glycan unit, or a combination thereof,b) contacting the mono- or disaccharides with any of the polymericcatalysts described herein and a suitable solvent (such as, e.g. wateror a non-aqueous solvent) for a period of time sufficient to produce apolymerized species population (with a desired average degree ofpolymerization); and c) isolating and/or recovering at least a portionof the polymerized glycan preparation.

In some embodiments, preparations of glycans (e.g. oligosaccharides) arepolymolecular. In some embodiments, preparations of glycans (e.g.oligosaccharides) are polymolecular and polydisperse. For example, theglycan therapeutic preparations comprise a mixture of distinctoligosaccharide species (e.g. of different degree of polymerization anddegree of branching and different alpha-to-beta glycosidic bond ratios).In some embodiments, the glycan therapeutic preparations comprise aplurality of distinct species (e.g. oligosaccharides) and may consist of1×10³, 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰, 1×10¹¹, 1×10¹²,1×10¹³, 1×10¹⁴, or more species in various proportions to each other.Herein described are the average properties of the glycan therapeuticpreparations, such as degree of polymerization, degree of branching,alpha- and beta-glycosidic bond ratios, etc.

In certain embodiments, the starting material (comprising the glycanunits) is contacted with a polymer catalyst under conditions thatpromote the formation of one or more glycosidic bond between glycanunits, thereby producing a preparation of glycans. In one embodiment,the glycan unit is a monosaccharide. In one embodiment, the glycan unitis a disaccharide. Suitable polymer catalysts comprise acidic monomersand ionic monomers that are connected to form a polymeric backbone,wherein each acidic monomer has at least one Bronsted-Lowry acid, andeach ionic monomer independently has at least one nitrogen-containingcationic group or phosphorous-containing cationic group. In someembodiments, each acidic monomer of the polymer catalyst may have oneBronsted-Lowry acid, and optionally the Bronsted-Lowry acids aredistinct. In some embodiments, each ionic monomer of the polymercatalyst has one nitrogen-containing cationic group orphosphorous-containing cationic group. In some embodiments, at least oneionic monomer of the polymer catalyst has two nitrogen-containingcationic groups or phosphorous-containing cationic groups. A schematicoutlining the general functional groups is shown in FIGS. 6 a and 6 b.

Generally, the polymeric catalyst and the glycan units are introducedinto an interior chamber of a reactor, either concurrently orsequentially. Glycan (e.g. oligosaccharides) synthesis can be performedin a batch process or a continuous process. For example, in oneembodiment, glycan synthesis is performed in a batch process, where thecontents of the reactor are continuously mixed or blended, and all or asubstantial amount of the products of the reaction are removed (e.g.isolated and/or recovered). In one variation, glycan synthesis isperformed in a batch process, where the contents of the reactor areinitially intermingled or mixed but no further physical mixing isperformed. In another variation, glycan synthesis is performed in abatch process, wherein once further mixing of the contents, or periodicmixing of the contents of the reactor, is performed (e.g., at one ormore times per hour), all or a substantial amount of the products of thereaction are removed (e.g. isolated and/or recovered) after a certainperiod of time.

In other embodiments, glycan (e.g. oligosaccharide) synthesis isperformed in a continuous process, where the contents flow through thereactor with an average continuous flow rate but with no explicitmixing. After introduction of the polymeric catalyst and glycan unitsinto the reactor, the contents of the reactor are continuously orperiodically mixed or blended, and after a period of time, less than allof the products of the reaction are removed (e.g. isolated and/orrecovered). In one variation, glycan synthesis is performed in acontinuous process, where the mixture containing the catalyst and glycanunits is not actively mixed. Additionally, mixing of catalyst and theglycan units may occur as a result of the redistribution of polymericcatalysts settling by gravity, or the non-active mixing that occurs asthe material flows through a continuous reactor.

In some embodiments of the method, the starting material for thepolymerization reaction is one or more glycan unit selected from one ormore monosaccharides, one or more disaccharides, or a combinationthereof. In some embodiments of the method, the starting material forthe polymerization reaction is one or more glycan unit selected from afuranose sugar and a pyranose sugar. In some embodiments of the method,the starting material for the polymerization reaction is one or moreglycan unit selected from a tetrose, a pentose, a hexose, or a heptose.In some embodiments of the method, the starting material for thepolymerization reaction is one or more glycan unit selected from aglucose, a galactose, an arabinose, a mannose, a fructose, a xylose, afucose, and a rhamnose, all optionally in either their L- or D-form, inalpha or beta configuration (for dimers), and/or a deoxy-form, whereapplicable, and any combination thereof. In some embodiments, the glycanunits are substituted or derivatized with one or more of an acetateester, sulfate half-ester, phosphate ester, or a pyruvyl cyclic acetalgroup, or have been otherwise derivatized at, e.g., at one or morehydroxyl groups.

The glycan units used in the methods described herein may include one ormore sugars. In some embodiments, the one or more sugars are selectedfrom monosaccharides, disaccharides, and trisaccharides, or any mixturesthereof. In some embodiments, the one or more sugars aremonosaccharides, such as one or more C5 or C6 monosaccharides. In someembodiments, the one or more sugars are C5 monosaccharides. In otherembodiments, the one or more sugars are C6 monosaccharides.

In some embodiments, the starting material for the polymerizationreaction is one or more glycan unit selected from monosaccharides andother carbohydrates including glycolaldehyde, glyceraldehyde,dihydroxyacetone, erythrose, threose, erythulose, arabinose, lyxose,ribose, xylose, ribulose, xylulose, allose, altrose, galactose, glucose,gulose, idose, mannose, talose, fructose, psicose, sorbose, tagatose,fucose, fuculose, rhamnose, mannoheptulose, sedoheptulose, neuraminicacid, N-acetylneuraminic acid, N-acetylgalactosamine,N-acetylglucosamine, fructosamine, galactosamine, glucosamine, sorbitol,glycerol, erythritol, threitol, arabitol, xylitol, mannitol, sorbitol,galactitol, fucitol, and lactic acid.

In some embodiments, the starting material for the polymerizationreaction is one or more glycan unit selected from a monosaccharide. Insome embodiments, the monosaccharide is glucose, galactose, fructose,fucose, mannose, arabinose, rhamnose, and xylose. In one embodiment, theglycan unit is not glucose. In one embodiment, the glycan unit is notgalactose. In one embodiment, the glycan unit is not fructose. In oneembodiment, the glycan unit is not fucose. In one embodiment, the glycanunit is not mannose. In one embodiment, the glycan unit is notarabinose. In one embodiment, the glycan unit is not rhamnose. In oneembodiment, the glycan unit is not xylose.

In some embodiments, the starting material for the polymerizationreaction is one or more glycan unit selected from disaccharides andother carbohydrates including acarviosin, N-acetyllactosamine,allolactose, cellobiose, chitobiose, glactose-alpha-1,3-galactose,gentiobiose, isomalt, isomaltose, isomaltulose, kojibiose, lactitol,lactobionic acid, lactose, lactulose, laminaribiose, maltitol, maltose,mannobiose, melibiose, melibiulose, neohesperidose, nigerose, robinose,rutinose, sambubiose, sophorose, sucralose, sucrose, sucrose acetateisobutyrate, sucrose octaacetate, trehalose, turanose, vicianose, andxylobiose.

In some embodiments, the starting material for the polymerizationreaction is one or more glycan unit selected from an amino sugar, adeoxy sugar, an imino sugar, a sugar acid, a short-chain fatty acid, anda sugar alcohol.

Suitable glycan units include amino sugars, such as, e.g. acarbose,N-acetylemannosamine, N-acetylmuramic acid, N-acetylneuraminic acid,N-acetyletalosaminuronic acid, arabinopyranosyl-N-methyl-N-nitrosourea,D-fructose-L-histidine, N-glycolyneuraminic acid, ketosamine, kidamycin,mannosamine, 1B-methylseleno-N-acetyl-D-galactosamine, muramic acid,muramyl dipeptide, phosphoribosylamine, PUGNAc, sialyl-Lewis A,sialyl-Lewis X, validamycin, voglibose, N-acetylgalactosamine,N-acetylglucosamine, aspartylglucosamine, bacillithiol, daunosamine,desosamine, fructosamine, galactosamine, glucosamine, meglumine, andperosamine.

Suitable glycan units include deoxy sugars, such as, e.g.1-5-ahydroglucitol, cladinose, colitose, 2-deoxy-D-glucose,3-deoxyglucasone, deoxyribose, dideoxynucleotide, digitalose,fludeooxyglucose, sarmentose, and sulfoquinovose.

Suitable glycan units include imino sugars, such as, e.g.castanospermine, 1-deoxynojirimycin, iminosugar, miglitol, miglustat,and swainsonine.

Suitable glycan units include sugar acids, such as, e.g.N-acetylneuraminic acid, N-acetyltalosamnuronic acid, aldaric acid,aldonic acid, 3-deoxy-D-manno-oct-2-ulosonic acid, glucuronic acid,glucosaminuronic acid, glyceric acid, N-glycolylneuraminic acid,iduronic acid, isosaccharinic acid, pangamic acid, sialic acid, threonicacid, ulosonic acid, uronic acid, xylonic acid, gluconic acid, ascorbicacid, ketodeoxyoctulosonic acid, galacturonic acid, galactosaminuronicacid, mannuronic acid, mannosaminuronic acid, tartaric acid, mucic acid,saccharic acid, lactic acid, oxalic acid, succinic acid, hexanoic acid,fumaric acid, maleic acid, butyric acid, citric acid, glucosaminic acid,malic acid, succinamic acid, sebacic acid, and capric acid.

Suitable glycan units include short-chain fatty acids, such as, e.g.,formic acid, acetic acid, propionic acid, butryic acid, isobutyric acid,valeric acid, and isovaleric acid.

Suitable glycan units include sugar alcohols, such as, e.g., methanol,ethylene glycol, glycerol, erythritol, threitol, arabitol, ribitol,xylitol, mannitol, sorbitol, galactitol, iditol, volemitol, fucitol,inositol, maltotritol, maltotetraitol, and polyglycitol.

In some embodiments, the glycan unit may exist as a salt (e.g., apharmaceutically acceptable salt), such as, e.g., a hydrochlorate,hydroiodate, hydrobromate, phosphate, sulfate, methanesulfate, acetate,formate, tartrate, malate, citrate, succinate, lactate, gluconate,pyruvate, fumarate, propionate, aspartate, glutamate, benzoate,ascorbate salt.

The glycan units used in the methods described herein may be obtainedfrom any commercially known sources, or produced according to anymethods known in the art.

Reaction Conditions

In some embodiments, the glycan units and catalyst (e.g., polymericcatalyst or solid-supported catalyst) are allowed to react for at least1 hour, at least 2 hours, at least 3 hours, at least 4 hours, at least 6hours, at least 8 hours, at least 16 hours, at least 24 hours, at least36 hours, or at least 48 hours; or between 1-24 hours, between 2-12hours, between 3-6 hours, between 1-96 hours, between 12-72 hours, orbetween 12-48 hours.

In some embodiments, the degree of polymerization (DP) of the glycanpreparation produced according to the methods described herein can beregulated by the reaction time. For example, in some embodiments, thedegree of polymerization of the glycan preparation is increased byincreasing the reaction time, while in other embodiments, the degree ofpolymerization of the glycan preparation is decreased by decreasing thereaction time.

Reaction Temperature

In some embodiments, the reaction temperature is maintained in the rangeof about 25° C. to about 150° C. In certain embodiments, the temperatureis from about 30° C. to about 125° C., about 60° C. to about 120° C.,about 80° C. to about 115° C., about 90° C. to about 110° C., about 95°C. to about 105° C., or about 100° C. to 110° C.

Amount of Glycan Units

The amount of the glycan unit used in the methods described hereinrelative to the amount solvent used may affect the rate of reaction andyield. The amount of the glycan unit used may be characterized by thedry solids content. In certain embodiments, dry solids content refers tothe total solids of a slurry as a percentage on a dry weight basis. Insome embodiments, the dry solids content of the glycan unit is betweenabout 5 wt % to about 95 wt %, between about 10 wt % to about 80 wt %,between about 15 wt %, to about 75 wt %, or between about 15 wt %, toabout 50 wt %.

Amount of Catalyst

The amount of the catalyst used in the methods described herein maydepend on several factors including, for example, the selection of thetype(s) of glycan unit, the concentration of the glycan unit, and thereaction conditions (e.g., temperature, time, and pH). In someembodiments, the weight ratio of the catalyst to the glycan unit(s) isabout 0.01 g/g to about 50 g/g, about 0.01 g/g to about 5 g/g, about0.05 g/g to about 1.0 g/g, about 0.05 g/g to about 0.5 g/g, about 0.05g/g to about 0.2 g/g, or about 0.1 g/g to about 0.2 g/g.

Solvent

In certain embodiments, synthesis of the glycans (e.g. oligosaccharides)using the polymeric catalyst is carried out in an aqueous environment.One suitable aqueous solvent is water. Generally, water with lowerconcentrations of ionic species is preferable, as such ionic species mayreduce the effectiveness of the polymeric catalyst. In some embodimentswhere the aqueous solvent is water, the water has less than 10% of ionicspecies (e.g., salts of sodium, phosphorous, ammonium, magnesium). Insome embodiments where the aqueous solvent is water, the water has aresistivity of at least 0.1 megaohm-centimeters, of at least 1megaohm-centimeters, of at least 2 megaohm-centimeters, of at least 5megaohm-centimeters, or of at least 10 megaohm-centimeters.

Water Content

In some embodiments, water is produced with each glycosidic bond formedbetween the one or more glycan units (dehydration reaction). In certainembodiments, the methods described herein may further include monitoringthe amount of water present in the reaction mixture and/or the ratio ofwater to glycan unit or catalyst over a period of time. In someembodiments, the method further includes removing at least a portion ofwater produced in the reaction mixture (e.g., by removing at least aboutany of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 99%, or100%, such as by vacuum filtration). It should be understood, however,that the amount of water to glycan unit may be adjusted based on thereaction conditions and specific catalyst used.

Any method known in the art may be used to remove water in the reactionmixture, including, for example, by vacuum filtration, vacuumdistillation, heating, and/or evaporation. In some embodiments, themethod comprises including water in the reaction mixture.

In some aspects, provided herein are methods of producing a glycanpreparation, by: combining a glycan unit and a catalyst having acidicand ionic moieties to form a reaction mixture, wherein water is producedin the reaction mixture; and removing at least a portion of the waterproduced in the reaction mixture. In certain variations, at least aportion of water is removed to maintain a water content in the reactionmixture of less than 99%, less than 90%, less than 80%, less than 70%,less than 60%, less than 50%, less than 40%, less than 30%, less than20%, less than 10%, less than 5%, or less than 1% by weight.

In some embodiments, the degree of polymerization of the glycanpreparation produced can be regulated by adjusting or controlling theconcentration of water present in the reaction mixture. For example, insome embodiments, the degree of polymerization of the glycan preparationis increased by decreasing the water concentration, while in otherembodiments, the degree of polymerization of the glycan preparation isdecreased by increasing the water concentration. In some embodiments,the water content of the reaction is adjusted during the reaction toregulate the degree of polymerization of the glycan preparationproduced.

For example, a majority, e.g. about 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 95%, or about 97% of the glycan therapeutic preparation has a DP ofbetween 2 and 25, between 3 and 25, between 4 and 25, between 5 and 25,between 6 and 25, between 7 and 25, between 8 and 25, between 9 and 25,between 10 and 25, between 2 and 30, between 3 and 30, between 4 and 30,between 5 and 30, between 6 and 30, between 7 and 30, between 8 and 30,between 9 and 30, or between 10 and 30.

In one example, to a round bottom flask equipped with an overheadstirrer and a jacketed short-path condenser one or more glycan units maybe added along with 1-50% (1-10%, 1-20%, 1-30%, 1-40%, 1-60%, 1-70%) bydry weight of one or more of the catalysts described herein. Water oranother compatible solvent (0.1-5 equiv, 1-5 equiv, 1-4 equiv, 0.1-4equiv) may be added to the dry mixture and the slurry can be combined atslow speed (e.g. 10-100 rpm, 50-200 rpm, 100-200 rpm) using a paddlesized to match the contours of the selected round bottom flask asclosely as possible. The mixture is heated to 70-180° C. (70-160° C.,75-165° C., 80-160° C.) under 10-1000 mbar vacuum pressure. The reactionmay be stirred for 30 minutes to 6 hours, constantly removing water fromthe reaction. Reaction progress can be monitored by HPLC.

The yield of conversion for the one or more glycan units in the methodsdescribed herein can be determined by any suitable method known in theart, including, for example, high performance liquid chromatography(HPLC). In some embodiments, the yield of conversion to a glycantherapeutic preparation with DP>1 after combining the one or more glycanunits with the catalyst (e.g., at 2, 3, 4, 8, 12, 24, or 48 hours aftercombining the one or more glycan units with the catalyst) is greaterthan about 50% (e.g., greater than about 55%, 60%, 65%, 70%, 75%, 80%,85%, 90%, 95%, or 98%). In some embodiments, the yield of conversion toa glycan therapeutic preparation with >DP2 after combining the one ormore glycan units with the catalyst (e.g., at 2, 3, 4, 8, 12, 24, or 48hours after combining the one or more glycan units with the catalyst) isgreater than 30% (e.g., greater than 35%, 40%, 45%, 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 95%, or 98%). In some embodiments, the yield ofconversion to a glycan therapeutic preparation with >DP3 after combiningthe one or more glycan units with the catalyst (e.g., at 2, 3, 4, 8, 12,24, or 48 hours after combining the one or more glycan units with thecatalyst) is greater than 30% (e.g., greater than 35%, 40%, 45%, 50%,55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 98%).

In some embodiments, the glycan therapeutic preparation has a degree ofpolymerization (DP) distribution after combining the one or more glycanunits with the polymeric catalyst (e.g., at 2, 3, 4, 8, 12, 24, or 48hours after combining the one or more glycan units with the catalyst)is: DP2=0%-40%, such as less than 40%, less than 30%, less than 20%,less than 10%, less than 5%, or less than 2%; or 10%-30% or 15%-25%;DP3=0%-20%, such as less than 15%, less than 10%, less than 5%; or5%-15%; and DP4+=greater than 15%, greater than 20%, greater than 30%,greater than 40%, greater than 50%; or 15%-75%, 20%-40% or 25%-35%.

The solid mass obtained by the process can be dissolved in a volume ofwater sufficient to create a solution of approximately 50 Brix (gramssugar per 100 g solution). Once dissolution is complete, the solidcatalyst can be removed by filtration. The solution comprisingtherapeutic glycans can be concentrated to about 50-75 Brix, e.g., byrotary evaporation. In some embodiments, the solution comprisingtherapeutic glycans can be concentrated to about 50-60 Brix, 60-70 Brix,70-80 Brix, 55-65 Brix, 65-75 Brix, or 75-85 Brix. In some embodiments,the solution comprising therapeutic glycans can be concentrated to about50, 55, 60, 65, 70, 75, 80, or about 85 Brix. Optionally, an organicsolvent can be used and water immiscible solvents can be removed bybiphasic extraction and water miscible solvents can be removed, e.g., byrotary evaporation concomitant to the concentration step.

Additional Processing Steps

Optionally, the glycan preparation produced may undergo additionalprocessing steps. Additional processing steps may include, for example,purification steps. Purification steps may include, for example,separation, dilution, concentration, filtration, desalting orion-exchange, chromatographic separation, or decolorization, or anycombination thereof.

Decolorization

In some embodiments, the methods described herein further include adecolorization step. The glycan preparation produced may undergo adecolorization step using any method known in the art, including, forexample, treatment with an absorbent, activated carbon, chromatography(e.g., using ion exchange resin), hydrogenation, and/or filtration(e.g., microfiltration).

In certain embodiments, the glycan preparations produced are contactedwith a color-absorbing material at a particular temperature, at aparticular concentration, and/or for a particular duration of time. Insome embodiments, the mass of the color absorbing species contacted withthe glycan preparation is less than 50% of the mass of the glycanpreparation, less than 35% of the mass of the glycan preparation, lessthan 20% of the mass of the glycan preparation, less than 10% of themass of the glycan preparation, less than 5% of the mass of the glycanpreparation, less than 2% of the mass of the glycan preparation, or lessthan 1% of the mass of the glycan preparation.

In some embodiments, the glycan preparations are contacted with a colorabsorbing material. In certain embodiments, the glycan preparations arecontacted with a color absorbing material for less than 10 hours, lessthan 5 hours, less than 1 hour, or less than 30 minutes. In a particularembodiment, the glycan preparations are contacted with a color absorbingmaterial for 1 hour.

In certain embodiments, the glycan preparations are contacted with acolor absorbing material at a temperature from about 20 to 100 degreesCelsius, about 30 to 80 degrees Celsius, about 40 to 80 degrees Celsius,or about 40 to 65 degrees Celsius. In a particular embodiment, theglycan preparations are contacted with a color absorbing material at atemperature of about 50 degrees Celsius.

In certain embodiments, the color absorbing material is activatedcarbon. In one embodiment, the color absorbing material is powderedactivated carbon. In other embodiments, the color absorbing material isan ion exchange resin. In one embodiment, the color absorbing materialis a strong base cationic exchange resin in a chloride form. In anotherembodiment, the color absorbing material is cross-linked polystyrene. Inyet another embodiment, the color absorbing material is cross-linkedpolyacrylate. In certain embodiments, the color absorbing material isAmberlite FPA91, Amberlite FPA98, Dowex 22, Dowex Marathon MSA, or DowexOptipore SD-2.

Ion-Exchange/De-Salting (Demineralization)

In some embodiments, the glycan preparations are contacted with amaterial to remove salts, minerals, and/or other ionic species. Incertain embodiments, the glycan preparations are flowed through ananionic/cationic exchange column pair. In one embodiment, the anionicexchange column contains a weak base exchange resin in a hydroxide formand the cationic exchange column contains a strong acid exchange resinin a protonated form.

Separation and Concentration

In some embodiments, the methods described herein further includeisolating the glycan preparation produced. In certain variations,isolating the glycan preparation comprises separating at least a portionof the glycan preparation from at least a portion of the catalyst, usingany method known in the art, including, for example, centrifugation,filtration (e.g., vacuum filtration, membrane filtration), and gravitysettling. In some embodiments, isolating the glycan preparationcomprises separating at least a portion of the glycan preparation fromat least a portion of any unreacted glycan units, using any method knownin the art, including, for example, filtration (e.g., membranefiltration), chromatography (e.g., chromatographic fractionation),differential solubility, and centrifugation (e.g., differentialcentrifugation).

In some embodiments, the methods further include a concentration step.For example, the isolated glycan preparations undergo evaporation (e.g.,vacuum evaporation) to produce a concentrated glycan preparation. Inother embodiments, the isolated glycan preparations undergo a spraydrying step to produce a powdered glycan preparation. In certainembodiments, the isolated glycan preparations undergo both anevaporation step and a spray drying step.

Fractionation

In some embodiments, glycan therapeutic preparations (e.g.oligosaccharides) are created that are polydisperse, exhibiting a rangeof degrees of polymerization. In some embodiments, the methods describedherein further include a fractionation step. Glycan species (e.g.,oligosaccharides) may be separated by molecular weight using any methodknown in the art, including, for example, high-performance liquidchromatography, adsorption/desorption (e.g. low-pressure activatedcarbon chromatography), or filtration (for example, ultrafiltration ordiafiltration). In certain embodiments, glycan species are separatedinto pools representing 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%,98%, or greater than 98% short (about DP1-2), medium (about DP3-10),long (about DP11-18), or very long (about DP>18) species.

In certain embodiments, glycan species are fractionated by adsorptiononto a carbonaceous material and subsequent desorption of fractions bywashing the material with mixtures of an organic solvent in water at aconcentration of 1%, 5%, 10%, 20%, 50%, or 100%. In one embodiment, theadsorption material is activated charcoal. In another embodiment, theadsorption material is a mixture of activated charcoal and a bulkingagent such as diatomaceous earth or Celite 545 in 5%, 10%, 20%, 30%,40%, or 50% portion by volume or weight.

In further embodiments, glycan species are separated by passage througha high-performance liquid chromatography system. In certain variations,glycan species are separated by ion-affinity chromatography, hydrophilicinteraction chromatography, or size-exclusion chromatography includinggel-permeation and gel-filtration.

In other embodiments, low molecular weight materials are removed byfiltration methods. In certain variations, low molecular weightmaterials may be removed by dialysis, ultrafiltration, diafiltration, ortangential flow filtration. In certain embodiments, the filtration isperformed in static dialysis tube apparatus. In other embodiments, thefiltration is performed in a dynamic flow filtration system. In otherembodiments, the filtration is performed in centrifugal force-drivenfiltration cartridges.

Characteristics of Glycan Therapeutic Preparations

The glycan therapeutics described herein may comprise oligosaccharidesand/or polysaccharides (referred to herein as “oligosaccharides”). Insome embodiments, the glycan therapeutics comprise homo-oligo- orpolymers (e.g., homoglycans), wherein all the glycan units in theoligomer or polymer are of the same type. Glycan therapeutics comprisinghomopolymers can include monosaccharides bonded together via a single ormultiple glycosidic bond types.

In some embodiments, the glycan therapeutics comprise hetero-oligo- orpolymers (e.g., heteroglycans), wherein more than one type of glycanunit is present. Glycan therapeutics comprising heteropolymers caninclude distinct types of monosaccharides bonded together via a singleor multiple glycosidic bond types.

In some embodiments, hydrolysis may be used to generate the constituentglycan units that are suitable to produce the glycans described herein.In one embodiment, the glycan unit is a monosaccharide. Monosaccharidesmay exist in many different forms, for example, conformers, cyclicforms, acyclic forms, stereoisomers, tautomers, anomers, and isomers.

Degree of Polymerization

In some embodiments, about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%,or about 97% of the glycan therapeutic preparation has a DP of at least5 and less than 30 glycan units. In some embodiments, about 55%, 60%,65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycantherapeutic preparation has a DP of at least 3 and less than 30 glycanunits. In some embodiments, about 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 95%, or about 97% of the glycan therapeutic preparation has a DP ofat least 3 and less than 25 glycan units. In some embodiments, about55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycantherapeutic preparation has a DP of at least 8 and less than 30 glycanunits. In some embodiments, about 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 95%, or about 97% of the glycan therapeutic preparation has a DP ofat least 10 and less than 30 glycan units. In some embodiments, about55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of the glycantherapeutic preparation has a DP of between 3, 4, 5, 6, 7, 8 and 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20 glycan units. In some embodiments,about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 97% of theglycan therapeutic preparation has a DP of between 10, 11, 12, 13, 14,15, 16, 17, 18, 19 and 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 glycanunits. In some embodiments, about 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 95%, or about 97% of the glycan therapeutic preparation has a DP ofbetween 3, 4, 5, 6, 7, 8, 9, 10 and 20, 21, 22, 23, 24, 25, 26, 27, 28glycan units.

In one embodiment, the glycan therapeutic preparation has a degree ofpolymerization (DP) of at least 3 and less than 30 glycan units. In oneembodiment, the glycan therapeutic preparation has a degree ofpolymerization (DP) of at least 5 and less than 30 glycan units. In oneembodiment, the glycan therapeutic preparation has a degree ofpolymerization (DP) of at least 3 and less than 25 glycan units.

In one embodiment, about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, orabout 97% of the glycan therapeutic preparation has a DP of at least 2.In one embodiment, about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, orabout 97% of the glycan therapeutic preparation has a DP of at least 3.

In some embodiments, glycan therapeutic preparations are provided,wherein at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, 99.8%, or atleast 99.9% or even 100% of the glycan therapeutic preparation has adegree of polymerization (DP) of at least 2, 3, 4, 5, 6, 7, 8, 9, 10,11, or at least 12 glycan units and less than 75, 70, 65, 60, 55, 50,45, 40, 35, 30, 25, 20, 19, 18, 17, 16, or less than 15 glycan units.

In some embodiments, glycan therapeutic preparations are provided,wherein at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, 99.8%, or atleast 99.9% or even 100% of the glycan therapeutic preparation has adegree of polymerization (DP) of at least 3 and less than 30 glycanunits, at least 5 and less than 30 glycan units, or at least 8 and lessthan 30 glycan units.

In some embodiments, about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%,or about 97% of the glycan therapeutic preparation has an average degreeof polymerization (DP) of about DP5, DP6, DP7, DP8, DP9, DP10, DP11,DP12, DP13, DP14, or DP15.

In some embodiments, glycan therapeutic preparations are providedwherein at least 50%, 60%, 70%, or 80% of the glycan therapeuticpreparation has a degree of polymerization of at least 3 and less than30 glycan units, or of at least 5 and less than 25 glycan units. In someembodiments, the average DP of the glycan therapeutic preparation isbetween about DP7 and DP9 or between about DP6 and DP10. In someembodiments, these glycan therapeutic preparations comprise an alpha- tobeta-glycosidic bond ratio from 0.8:1 to 5:1 or from 1:1 to 4:1. In someembodiments, the fractionated preparations have an average degree ofbranching of between about 0.01 and about 0.2 or between about 0.05 and0.1.

In one embodiment, a polydisperse, fractionated glycan therapeuticpreparation is provided comprising at least 85%, 90%, or at least 95%medium-length species with a DP of about 3-10. In one embodiment, apolydisperse, fractionated glycan therapeutic preparation is providedcomprising at least 85%, 90%, or at least 95% long-length species with aDP of about 11-18. In one embodiment, a polydisperse, fractionatedglycan therapeutic preparation is provided comprising at least 85%, 90%,or at least 95% very long-length species with a DP of about 18-30. Insome embodiments, the medium, long and very long fractionatedpreparations comprise an alpha- to beta-glycosidic bond ratio from 0.8:1to 5:1 or from 1:1 to 4:1. In some embodiments, the fractionatedpreparations have an average degree of branching of between about 0.01and about 0.2 or between about 0.05 and 0.1.

In some embodiments, about 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%,or about 97% of the glycan therapeutic preparation has an averagemolecular weight of about 500, 550, 600, 650, 700, 750, 800, 850, 900,950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500,1550, 1600, 1650, 1700, 1750, 1800 g/mol and less than 1900, 2000, 2100,2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300,3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500,4600, 4700, 4800, 4900, and 5000 g/mol.

Degree of Branching

In some embodiments, the glycan preparations (e.g. oligosaccharides)range in structure from linear to highly branched. Unbranched glycansmay contain only alpha linkages or only beta linkages. Unbranchedglycans may contain at least one alpha and at least one beta linkage.Branched glycans may contain at least one glycan unit being linked viaan alpha or a beta glycosidic bond so as to form a branch. The branchingrate or degree of branching (DB) may vary, such that about every 2^(nd),3^(rd), 4^(th), 5^(th), 6^(th), 7^(th), 8^(th), 9^(th), 10^(th),15^(th), 20^(th), 25^(th), 30^(th), 35^(th), 40^(th), 45^(th), 50^(th),60^(th), or 70^(th) unit comprises at least one branching point. Forexample, animal glycogen contains a branching point approximately every10 units.

In some embodiments, preparations of glycan therapeutics are provided,wherein the preparation comprises a mixture of branched glycans, whereinthe average degree of branching (DB, branching points per residue) is 0,0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.2, 0.3,0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 0.99, 1, or 2. In some embodiments,preparations of glycan therapeutics are provided, wherein the averagedegree of branching is at least 0.01, 0.05, 0.1, 0.2, 0.3, or at least0.4. In some embodiments, preparations of glycan therapeutics areprovided, wherein the average degree of branching is between about 0.01and 0.1, 0.01 and 0.2, 0.01 and 0.3, 0.01 and 0.4, or 0.01 and 0.5. Insome embodiments, preparations of glycan therapeutics are provided,wherein the average degree of branching is between about 0.05 and 0.1,0.05 and 0.2, 0.05 and 0.3, 0.05 and 0.4, or 0.05 and 0.5. In someembodiments, preparations of glycan therapeutics are provided, whereinthe average degree of branching is between about 0.1 and 0.2, 0.1 and0.3, 0.1 and 0.4, or 0.1 and 0.5. In some embodiments, preparations ofglycan therapeutics are provided, wherein the average degree ofbranching is not 0. In some embodiments, preparations of glycantherapeutics are provided, wherein the average degree of branching isnot between at least 0.1 and less than 0.4 or at least 0.2 and less than0.4. In some embodiments, the preparations of glycan therapeuticscomprise linear glycans. In some embodiments, the preparations of glycantherapeutics comprise glycans that exhibit a branched orbranch-on-branch structure, e.g., branched glycans (such as, e.g.,branched oligosaccharides and/or branched polysaccharides).

In some embodiments, preparations of glycan therapeutics are providedwherein the average degree of branching (DB) is not 0, but is at least0.01, 0.05, 0.1, or at least 0.2, or ranges between about 0.01 and about0.2 or between about 0.05 and 0.1.

Glycosidic Linkages

The linkage or bonds between two glycan units can be expressed, forexample, as 1,4, 1 →4, or (1-4), used interchangeably and are referredto herein as glycosidic linkages or bonds for compounds comprising oneor more sugars (e.g. monosaccharides, disaccharides and the like).Monosaccharides can be in the cyclic form (e.g. pyranose or furanoseform). For example, lactose is a disaccharide composed of cyclic formsof galactose and glucose joined by a beta (1-4) linkage where the acetaloxygen bridge is in the beta orientation.

Linkages or bonds between the individual glycan units found inpreparations of glycan therapeutics may include one or more (e.g., twoor more, three or more, four or more, five or more, six or more, etc.)of alpha 1 →2, alpha 1 →3, alpha 1 →4, alpha 1 →6, alpha 2 →1, alpha 2→3, alpha 2 →4, alpha 2 →6, beta 1 →2, beta 1 →3, beta 1 →4, beta 1 →6,beta 2 →1, beta 2 →3, beta 2 →4, and beta 2 →6.

In some embodiments, the glycan therapeutic preparation comprises bothalpha- and beta-glycosidic bonds selected from the group consisting of 1→2 glycosidic bond, a 1 →3 glycosidic bond, a 1 →4 glycosidic bond, a 1→5 glycosidic bond and a 1 →6 glycosidic bond. In some embodiments, theglycan therapeutic preparation comprises at least two or at least threealpha and beta 1 →2 glycosidic bonds, alpha and beta 1 →3 glycosidicbonds, alpha and beta 1 →4 glycosidic bonds, alpha and beta 1 →5glycosidic bonds, and/or alpha and beta 1 →6 glycosidic bonds.

In some embodiments, the glycan therapeutic preparations comprise onlyalpha linkages. In some embodiments, the glycan therapeutics compriseonly beta linkages. In some embodiments, the glycan therapeuticscomprise mixtures of alpha and beta linkages.

In some embodiments, the alpha:beta glycosidic bond ratio in apreparation is about 0.1:1, 0.2:1, 0.3:1, 0.4:1, 0.5:1, 0.6:1, 0.7:1,0.8:1, 0.9:1, 1:1, 1.2:1, 1.5:1, 1.7:1, 2:1, 2.2:1, 2.5:1, 2.7:1, 3:1,4:1, 5:1, 6:1, 7:1, 8:1, 9:1, or about 10:1.

In some embodiments, the glycan therapeutic preparations comprise andalpha:beta glycosidic bond ratio in a preparation of about 0.8:1, 1:1,2:1, 3:1, 4:1 or 5:1, or it ranges from about 0.8:1 to about 5:1 or fromabout 1:1 to about 4:1.

In some embodiments, the preparations of glycan therapeutics (e.g.oligosaccharides) comprises substantially all alpha- or beta configuredglycan units, optionally comprising about 1%, 2%, 3%, 4% 5%, 6%, 7%, 8%,9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, or 20% of therespective other configuration.

In some embodiments, the preparations of glycan therapeutics comprise atleast 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%,40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,99%, at least 99.9% or even 100% glycans with alpha glycosidic bonds. Insome embodiments, the preparations of glycan therapeutics comprise atleast 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%,40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%,99%, at least 99.9% or even 100% glycans with beta glycosidic bonds. Insome embodiments, preparations of glycan therapeutics are provided,wherein at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%,65%, 70%, 75%, 80%, or at least 85% of glycans with glycosidic bondsthat are alpha glycosidic bonds, at least 10%, 15%, 20%, 25%, 30%, 35%,40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, or at least 85% of glycanswith glycosidic bonds that are beta glycosidic bonds, and wherein thepercentage of alpha and beta glycosidic bonds does not exceed 100%.

In some embodiments, preparations of glycan therapeutics are provided,wherein at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%,30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%,97%, 98%, 99%, at least 99.9% or even 100% of glycan glycosidic bondsare one or more of: 1 →2 glycosidic bonds, 1 →3 glycosidic bonds, 1 →4glycosidic bonds, and 1 →6 glycosidic bonds. In some embodiments,preparations of glycan therapeutics are provided, wherein at least 1%,2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, at least 20%, or 25% each ofglycan glycosidic bonds are 1 →2, 1 →3, 1 →4, and 1 →6 glycosidic bonds.Optionally, the preparations of glycan therapeutics further comprise atleast 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%,40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, or at least 85% of glycanglycosidic bonds that are selected from the group consisting of: alpha 2→1, alpha 2 →3, alpha 2 →4, alpha 2 →6, beta 2 →1, beta 2 →3, beta 2 →4,and beta 2 →6, glycosidic bonds.

In some embodiments, the preparations of glycan therapeutics compriseglycans with at least two glycosidic bonds selected from the groupconsisting of alpha 1 →2 and alpha 1 →3, alpha 1 →2 and alpha 1 →4,alpha 1 →2 and alpha 1 →6, alpha 1 →2 and beta 1 →2, alpha 1 →2 and beta1 →3, alpha 1 →2 and beta 1 →4, alpha 1 →2 and beta 1 →6, alpha 1 →3 andalpha 1 →4, alpha 1 →3 and alpha 1 →6, alpha 1 →3 and beta 1 →2, alpha 1→3 and beta 1 →3, alpha 1 →3 and beta 1 →4, alpha 1 →3 and beta 1 →6,alpha 1 →4 and alpha 1 →6, alpha 1 →4 and beta 1 →2, alpha 1 →4 and beta1 →3, alpha 1 →4 and beta 1 →4, alpha 1 →4 and beta 1 →6, alpha 1 →6 andbeta 1 →2, alpha 1 →6 and beta 1 →3, alpha 1 →6 and beta 1 →4, alpha 1→6 and beta 1 →6, beta 1 →2 and beta 1 →3, beta 1 →2 and beta 1 →4, beta1 →2 and beta 1 →6, beta 1 →3 and beta 1 →4, beta 1 →3 and beta 1 →6,and beta 1 →4 and beta 1 →6.

For preparations comprising branched glycan therapeutics (e.g. thosewith a DB of 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1,0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 0.99, 1, or 2) comprisinga side chain, which can be the same or a different side chain, the sidechain may be attached via one or more beta and alpha linkages, such as(1-2), (1-3), (1-4), (1-6), (2-3), (2-6) or other suitable linkages tothe main chain.

Glycan Units

In some embodiments, preparations of glycan therapeutics are provided,wherein at least one glycan unit is a sugar in L-form. In someembodiments, preparations of glycans are provided, wherein at least oneglycan unit is a sugar in D-form. In some embodiments, preparations ofglycans are provided, wherein the glycan units are sugars in L- orD-form as they naturally occur or are more common (e.g. D-glucose,D-xylose, L-arabinose).

In some embodiments, the preparation of glycan therapeutics (e.g.oligosaccharides) comprises a desired mixture of L- and D-forms ofglycan units, e.g. of a desired ratio, such as: 1:1, 1:2, 1:3, 1:4, 1:5,1:6, 1:7, 1:8, 1:9, 1:10, 1:12, 1:14, 1:16, 1:18, 1:20, 1:25, 1:30,1:35, 1:40, 1:45, 1:50, 1:55, 1:60, 1:65, 1:70, 1:75, 1:80, 1:85, 1:90,1:100, 1:150 L- to D-forms or D- to L-forms.

In some embodiments, the preparation of glycan therapeutics comprisesglycans with substantially all L- or D-forms of glycan units, optionallycomprising about 1%, 2%, 3%, 4% 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%,14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% ofthe respective other form.

In some embodiments, preparations of glycan therapeutics are provided,wherein at least one glycan unit is a diose, triose, tetrose, a pentose,a hexose, or a heptose. Optionally, the glycan units involved in theformation of the glycans are varied. Examples of monosaccharide glycanunits include hexoses, such as glucose, galactose, and fructose, andpentoses, such as xylose. The monosaccharide glycan units may exist inan acyclic (open-chain) form. Open-chain monosaccharides with samemolecular graph may exist as two or more stereoisomers. Themonosaccharides may also exist in a cyclic form through a nucleophilicaddition reaction between the carbonyl group and one of the hydroxyls ofthe same molecule. The reaction creates a ring of carbon atoms closed byone bridging oxygen atom. In these cyclic forms, the ring usually has 5(furanoses) or 6 atoms (pyranoses).

In some embodiments, the preparation of glycan therapeutics (e.g.oligosaccharides) comprises a desired mixture of differentmonosaccharide glycan units, such as a mixture of a diose, a triose,tetrose, pentose, hexose, or heptose, including any mixtures of two ormore pentoses (e.g., arabinose and xylose) and mixtures of two or morehexoses (e.g., glucose and galactose), in any desired ratio, e.g. forany two glycan units: 1:1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1:10,1:12, 1:14, 1:16, 1:18, 1:20, 1:25, 1:30, 1:35, 1:40, 1:45, 1:50, 1:55,1:60, 1:65, 1:70, 1:75, 1:80, 1:85, 1:90, 1:100, 1:150, etc., for anythree glycan units: 1:1:1, 1:2:1, 1:3:1, 1:4:1, 1:5:1, 1:6:1, 1:7:1,1:8:1, 1:9:1, 1:10:1, 1:12:1, 1:14:1, 1:16:1, 1:18:1, 1:20:1, 1:1:2,1:2:2, 1:3:2, 1:4:2, 1:5:2, 1:6:2, 1:7:2, 1:8:2, 1:9:2, 1:10:2, 1:1:3,1:2:3, 1:3:3, 1:4:3, 1:5:3, 1:6:3, 1:7:3, 1:8:3, 1:9:3, 1:10:3, 1:1:4,1:2:4, 1:3:4, 1:4:4, 1:5:4, 1:6:4, 1:7:4, 1:8:4, 1:9:4, 1:10:4, 1:1:5,1:2:5, 1:3:5, 1:4:5, 1:5:5, 1:6:5, 1:7:5, 1:8:5, 1:9:5, 1:10:5, etc.,for any four glycan units: 1:1:1:1, 1:2:2:1, 1:3:2:1, 1:4:2:1, 1:5:2:1,1:6:2:1, 1:7:2:1, 1:8:2:1, 1:9:2:1, 1:10:2:1, 1:1:1:2, 1:2:2:2, 1:3:2:2,1:4:2:2, 1:5:2:2, 1:6:2:2, 1:7:2:2, 1:8:2:2, 1:9:2:2, 1:10:2:2, etc.,for any five glycan units: 1:1:1:1:1, 1:2:2:1:1, etc., for any sixglycan units: 1:1:1:1:1:1, 1:1:1:1:1:2, etc., for any seven glycanunits: 1:1:1:1:1:1:1, 1:1:1:1:1:1:2, etc., and so on.

In some embodiments, the preparation of glycan therapeutics comprises adesired mixture of two, three, four or five different glycan units, suchas a mixture of, e.g., i) one or more glycan units selected frommonosaccharides, selected from glucose, galactose, arabinose, mannose,fructose, xylose, fucose, and rhamnose; ii) one or more glycan unitsselected from disaccharides selected from acarviosin,n-acetyllactosamine, allolactose, cellobiose, chitobiose,galactose-alpha-1,3-galactose, gentiobiose, isomalt, isomaltose,isomaltulose, kojibiose, lactitol, lactobionic acid, lactose, lactulose,laminaribiose, maltitol, maltose, mannobiose, melibiose, melibiulose,neohesperidose, nigerose, robinose, rutinose, sambubiose, sophorose,sucralose, sucrose, sucrose acetate isobutyrate, sucrose octaacetate,trehalose, turanose, vicianose, and xylobiose; iii) one or more glycanunits selected from amino sugars selected from acarbose,N-acetylemannosamine, N-acetylmuramic acid, N-acetylnueraminic acid,N-acetyletalosaminuronic acid, arabinopyranosyl-N-methyl-N-nitrosourea,D-fructose-L-histidine, N-glycolyneuraminic acid, ketosamine, kidamycin,mannosamine, 1B-methylseleno-N-acetyl-D-galactosamine, muramic acid,muramyl dipeptide, phosphoribosylamine, PUGNAc, sialyl-Lewis A,sialyl-Lewis X, validamycin, voglibose, N-acetylgalactosamine,N-acetylglucosamine, aspartylglucosamine, bacillithiol, daunosamine,desosamine, fructosamine, galactosamine, glucosamine, meglumine, andperosamine; iv) one or more glycan units selected from deoxy sugarsselected from 1-5-ahydroglucitol, cladinose, colitose,2-deoxy-D-glucose, 3-deoxyglucasone, deoxyribose, dideoxynucleotide,digitalose, fludeooxyglucose, sarmentose, and sulfoquinovose; v) one ormore glycan units selected from imino sugars selected fromcastanospermine, 1-deoxynojirimycin, iminosugar, miglitol, miglustat,and swainsonine; one or more glycan units selected from sugar acidsselected from N-acetylneuraminic acid, N-acetyltalosamnuronic acid,aldaric acid, aldonic acid, 3-deoxy-D-manno-oct-2-ulosonic acid,glucuronic acid, glucosaminuronic acid, glyceric acid,N-glycolylneuraminic acid, iduronic acid, isosaccharinic acid, pangamicacid, sialic acid, threonic acid, ulosonic acid, uronic acid, xylonicacid, gluconic acid, ascorbic acid, ketodeoxyoctulosonic acid,galacturonic acid, galactosaminuronic acid, mannuronic acid,mannosaminuronic acid, tartaric acid, mucic acid, saccharic acid, lacticacid, oxalic acid, succinic acid, hexanoic acid, fumaric acid, maleicacid, butyric acid, citric acid, glucosaminic acid, malic acid,succinamic acid, sebacic acid, and capric acid; vi) one or more glycanunits selected from short-chain fatty acids selected from formic acid,acetic acid, propionic acid, butryic acid, isobutyric acid, valericacid, and isovaleric acid; and vii) one or more glycan units selectedfrom sugar alcohols selected from methanol, ethylene glycol, glycerol,erythritol, threitol, arabitol, ribitol, xylitol, mannitol, sorbitol,galactitol, iditol, volemitol, fucitol, inositol, maltotritol,maltotetraitol, and polyglycitol.

In some embodiments, the preparation of glycan therapeutics comprises aglycan unit or plurality of glycan units present in a salt form (e.g., apharmaceutically acceptable salt form), such as, e.g., a hydrochlorate,hydroiodate, hydrobromate, phosphate, sulfate, methanesulfate, acetate,formate, tartrate, malate, citrate, succinate, lactate, gluconate,pyruvate, fumarate, propionate, aspartate, glutamate, benzoate,ascorbate salt.

Exemplary glycans are described by a three-letter code representing themonomeric sugar component followed by a number out of one hundredreflecting the percentage of the material that monomer constitutes.Thus, ‘glu100’ is ascribed to a glycan generated from a 100% D-glucose(glycan unit) input and ‘glu50gal50’ is ascribed to a glycan generatedfrom 50% D-glucose and 50% D-galactose (glycan units) input or,alternatively from a lactose dimer (glycan unit) input. As used herein:xyl=D-xylose; ara=L-arabinose; gal=D-galactose; glu=D-glucose;rha=L-rhamnose; fuc=L-fucose; man=D-mannose; sor=D-sorbitol;gly=D-glycerol; neu=NAc-neuraminic acid.

In some embodiments, the preparation of glycan therapeutics comprisesone glycan unit A selected from i) to vii) above, wherein glycan unit Acomprises 100% of the glycan unit input. For example, in someembodiments, the glycan therapeutic preparation is selected from thehomo-glycans xyl100, rha100, ara100, gal100, glu100, and man100. In someembodiments, the glycan therapeutic preparation is selected from thehomo-glycans fuc100 and fru100. In some embodiments, the glycantherapeutic preparation comprises man100.

In some embodiments, the preparation of glycan therapeutics comprises amixture of two glycan units A and B selected independently from i) tovii) above, wherein A and B may be selected from the same or a differentgroup i) to vii) and wherein A and B may be selected in any desiredratio (e.g. anywhere from 1-99% A and 99-1% B, not exceeding 100%).

For example, in some embodiments, the glycan therapeutic preparation isselected from the hetero-glycans ara50gal50, xyl75gal25, ara80xyl20,ara60xyl40, ara50xyl50, glu80man20, glu60man40, man60glu40, man80glu20,gal75xyl25, glu50gal50, man62glu38, and the hybrid glycans glu90sor10and glu90gly10.

In some embodiments, the preparation of glycan therapeutics comprises amixture of three glycan units A, B and C selected independently from i)to vii) above, wherein A, B and C may be selected from the same or adifferent group i) to vii) and wherein A, B and C may be selected in anydesired ratio (e.g. anywhere from 1-99% A, 1-99% B, 1-99% C, notexceeding 100%).

For example, in some embodiments, the glycan therapeutic preparation isselected from the hetero-glycans xyl75glu12gal12, xyl33glu33gal33,glu33gal33fuc33, man52glu29gal19, and the hybrid glycan glu33gal33neu33.

In some embodiments, the preparation of glycan therapeutics comprises amixture of four glycan units A, B, C and D selected independently fromi) to vii) above, wherein A, B, C and D may be selected from the same ora different group i) to vii) and wherein A, B, C and D may be selectedin any desired ratio (e.g. anywhere from 1-99% A, 1-99% B, 1-99% C,1-99% D, not exceeding 100%).

In some embodiments, the preparation of glycan therapeutics comprises amixture of five glycan units A, B, C, D and E selected independentlyfrom i) to vii) above, wherein A, B, C, D and E may be selected from thesame or a different group i) to vii) and wherein A, B, C, D and E may beselected in any desired ratio (e.g. anywhere from 1-99% A, 1-99% B,1-99% C, 1-99% D, 1-99% E, not exceeding 100%).

In some embodiments, preparations of glycan therapeutics are provided,wherein at least one glycan unit is selected from the group consistingof a glucose, a galactose, an arabinose, a mannose, a fructose, axylose, a fucose, and a rhamnose. In one embodiment, the glycan unit isnot glucose. In one embodiment, the glycan unit is not galactose. In oneembodiment, the glycan unit is not fructose. In one embodiment, theglycan unit is not fucose. In one embodiment, the glycan unit is notmannose. In one embodiment, the glycan unit is not arabinose. In oneembodiment, the glycan unit is not rhamnose. In one embodiment, theglycan unit is not xylose.

In some embodiments, the preparation of glycan therapeutics comprises adesired mixture of two different monosaccharide glycan units, such as amixture of, e.g., glucose and galactose, glucose and arabinose, glucoseand mannose, glucose and fructose, glucose and xylose, glucose andfucose, glucose and rhamnose, galactose and arabinose, galactose andmannose, galactose and fructose, galactose and xylose, galactose andfucose, and galactose and rhamnose, arabinose and mannose, arabinose andfructose, arabinose and xylose, arabinose and fucose, and arabinose andrhamnose, mannose and fructose, mannose and xylose, mannose and fucose,and mannose and rhamnose, fructose and xylose, fructose and fucose, andfructose and rhamnose, xylose and fucose, xylose and rhamnose, andfucose and rhamnose, etc., e.g. a in a ratio of 1:1, 1:2, 1:3, 1:4, 1:5,1:6, 1:7, 1:8, 1:9, 1:10, 1:12, 1:14, 1:16, 1:18, 1:20, 1:25, 1:30,1:35, 1:40, 1:45, 1:50, 1:55, 1:60, 1:65, 1:70, 1:75, 1:80, 1:85, 1:90,or 1:100 or the reverse ratio thereof.

In some embodiments, the preparation of glycan therapeutics (e.g.oligosaccharides) comprises a desired mixture of three differentmonosaccharide glycan units, such as a mixture of, e.g. forglucose-containing glycan-therapeutic preparations, glucose, galactoseand arabinose; glucose, galactose and mannose; glucose, galactose andfructose; glucose, galactose and xylose; glucose, galactose and fucose,glucose, galactose and rhamnose; glucose, arabinose, and mannose;glucose, arabinose and fructose; glucose, arabinose and xylose; glucose,arabinose and fucose; glucose, arabinose and rhamnose; glucose, mannoseand fructose; glucose, mannose and xylose; glucose, mannose and fucose;glucose, mannose rhamnose; glucose, fructose and xylose; glucose,fructose and fucose; glucose, fructose and rhamnose; glucose, fucose andrhamnose, etc., e.g. a in a ratio of 1:1:1, 1:2:1, 1:3:1, 1:4:1, 1:5:1,1:6:1, 1:7:1, 1:8:1, 1:9:1, 1:10:1, 1:12:1, 1:14:1, 1:16:1, 1:18:1,1:20:1, 1:1:2, 1:2:2, 1:3:2, 1:4:2, 1:5:2, 1:6:2, 1:7:2, 1:8:2, 1:9:2,1:10:2, 1:1:3, 1:2:3, 1:3:3, 1:4:3, 1:5:3, 1:6:3, 1:7:3, 1:8:3, 1:9:3,1:10:3, 1:1:4, 1:2:4, 1:3:4, 1:4:4, 1:5:4, 1:6:4, 1:7:4, 1:8:4, 1:9:4,1:10:4, 1:1:5, 1:2:5, 1:3:5, 1:4:5, 1:5:5, 1:6:5, 1:7:5, 1:8:5, 1:9:5,1:10:5, etc.

In some embodiments, preparations of glycan therapeutics are provided,wherein at least one glycan unit is a furanose sugar. In someembodiments, preparations of glycans are provided, wherein at least oneglycan unit is a pyranose sugar. In some embodiments, glycantherapeutics comprise mixtures of furanose and pyranose sugars. In someembodiments, the furanose: pyranose sugar ratio in a preparation isabout 0.1:1, 0.2:1, 0.3:1, 0.4:1, 0.5:1, 0.6:1, 0.7:1, 0.8:1, 0.9:1,1:1, 1.2:1, 1.5:1, 1.7:1, 2:1, 2.2:1, 2.5:1, 2.7:1, 3:1, 4:1, 5:1, 6:1,7:1, 8:1, 9:1, or about 10:1.

In some embodiments, the preparation of glycan therapeutics (e.g.oligosaccharides) comprises a desired mixture of furanose and pyranosesugars, e.g. of a desired ratio, such as: 1:1, 1:2, 1:3, 1:4, 1:5, 1:6,1:7, 1:8, 1:9, 1:10, 1:12, 1:14, 1:16, 1:18, 1:20, 1:25, 1:30, 1:35,1:40, 1:45, 1:50, 1:55, 1:60, 1:65, 1:70, 1:75, 1:80, 1:85, 1:90, 1:100,1:150 furanose to and pyranose or pyranose to furanose.

In some embodiments, the preparation of glycan therapeutics comprisessubstantially all furanose or pyranose sugar, optionally comprising 1%,2%, 3%, 4% 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%,18%, 19%, or 20% of the respective other sugar.

In some embodiments, the preparation of glycan therapeutics comprisessubstantially all pyranose sugar and no more than about 0.1%, 02%, 0.5%,1%, 2%, 3%, 4%, or no more than 5% of monomeric glycan units in thepreparation in furanose form. In some embodiments, no more than 3%, 2%or no more than 1% of monomeric glycan units in the preparation are infuranose form.

In some embodiments, the preparation of glycan therapeutics does notcomprise N-acetylgalactosamine or N-acetylglucosamine. In someembodiments, the preparation of glycans does not comprise sialic acid.In some embodiments, the preparation of glycan therapeutics does notcomprise a lipid and fatty acid. In some embodiments, the preparation ofglycan therapeutics does not comprise an amino acid.

In some embodiments, the preparation of glycan therapeutics does notcomprise a detectable repeating unit. In some embodiments, thepreparation of glycan therapeutics does not comprise a statisticallysignificant amount of a repeating unit. In some embodiments, therepeating unit has a DP of at least 2, 3, 4, 5, or at least 6 glycanunits. For example, hyaluronan is a glycosaminoglycan with a repeatingdisaccharide unit consisting of two glucose derivatives, glucuronate(glucuronic acid) and N-acetylglucosamine. The glycosidic linkages arebeta (1 →3) and beta (1 →4). Cellulose is a polymer made with repeatedglucose units linked together by beta-linkages. The presence and amountof repeating units can be determined, e.g. using by total hydrolysis(e.g. to determine the proportion of glycan units), methylation analysis(e.g. to determine the distribution of bond types), and HSQC (e.g. todetermine the distribution of alpha- and beta-glycosides). Statisticalmethods to determine significance are known by one of skill in the art.

If desired, the monosaccharide or oligosaccharide glycan units of theglycans are further substituted or derivatized, e.g., hydroxyl groupscan be etherified or esterified. For example, the glycans (e.g.oligosaccharide) can contain modified saccharide units, such as2′-deoxyribose wherein a hydroxyl group is removed, 2′-fluororibosewherein a hydroxyl group is replace with a fluorine, orN-acetylglucosamine, a nitrogen-containing form of glucose (e.g.,2′-fluororibose, deoxyribose, and hexose). The degree of substitution(DS, average number of hydroxyl groups per glycosyl unit) can be 1, 2,or 3, or another suitable DS. In some embodiments, 1%, 2%, 3%, 4% 5%,6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 80%, 85%, 90%, 95%,96%, 97%, 98%, 99%, or 100% of glycan units are substituted orderivatized. In some embodiments, the degree of substitution variesbetween subunits, e.g., a certain percentage is not derivatized,exhibits a DS of 1, exhibits a DS of 2, or exhibits a DS of 3. Anydesired mixture can be generated, e.g. 0-99% of subunits are notderivatized, 0-99% of subunits exhibit a DS of 1, 0-99% of subunitsexhibit a DS of 2, and 0-99% of subunits exhibit a DS of 3, with thetotal making up 100%. The degree of substitution can be controlled byadjusting the average number of moles of substituent added to a glycosylmoiety (molar substitution (MS)). The distribution of substituents alongthe length of the glycan oligo- and polysaccharide chain can becontrolled by adjusting the reaction conditions, reagent type, andextent of substitution. In some embodiments, the monomeric subunits aresubstituted with one or more of an acetate ester, sulfate half-ester,phosphate ester, or a pyruvyl cyclic acetal group.

Solubility

In some embodiments, the glycan therapeutic preparations are highlybranched, e.g. have an average DB of at least 0.01, 0.05, or 0.1. Insome embodiments, the glycan therapeutic preparations have an average DBof about 0.01 to about 0.05, 0.01 to 0.1, 0.05 to 0.1, or about 0.1 toabout 0.2. In some embodiments, the glycan therapeutic preparationscomprising branched oligosaccharide are highly soluble. In someembodiments, glycan therapeutic preparations can be concentrated to atleast to 55 Brix, 65 Brix, 60 Brix, 65 Brix, 70 Brix, 75 Brix, 80 Brix,or at least 85 Brix without obvious solidification or crystallization at23° C. (final solubility limit). In some embodiments, glycan therapeuticpreparations can be concentrated to about 50-60 Brix, 60-70 Brix, 70-80Brix, 55-65 Brix, 65-75 Brix, or to about 75-85 Brix. In someembodiments, glycan therapeutic preparations can be concentrated toabout 50, 55, 60, 65, 70, 75, 80, or about 85 Brix without obvioussolidification or crystallization at 23° C. (final solubility limit).

In some embodiments, glycan therapeutic preparations are concentrated toat least about 0.5 g/ml, 1 g/ml, 1.5 g/ml, 2 g/ml, 2.5 g/ml, 3 g/ml, 3.5g/ml or at least 4 g/ml without obvious solidification orcrystallization at 23° C. (final solubility limit).

In some embodiments, the glycan therapeutic preparations (e.g.oligosaccharides) are branched, e.g. have an average DB of at least0.01, 0.05, or 0.1 and has a final solubility limit in water of at leastabout 70 Brix, 75 Brix, 80 Brix, or at least about 85 Brix at 23° C. oris at least about 1 g/ml, 2 g/ml or at least about 3 g/ml.

In some embodiments, the preparation of glycan therapeutics has a finalsolubility limit of at least 0.001 g/L, 0.005 g/L, 0.01 g/L, 0.05 g/L,0.1 g/L, 0.2 g/L, 0.3 g/L, 0.4 g/L, 0.5 g/L, 0.6 g/L, 0.7 g/L, 0.8 g/L,0.9 g/L, 1 g/L, 5 g/L, 10 g/L, 20 g/L, 30 g/L, 40 g/L, 50 g/L, 100 g/L,200 g/L, 300 g/L, 400 g/L, 500 g/L, 600 g/L, 700 g/L, 800 g/L, 900 g/L,1000 g/L in deionized water, or in a suitable buffer such as, e.g.,phosphate-buffered saline, pH 7.4 or similar physiological pH and at 20°C. In some embodiments, the preparation of glycan therapeutics isgreater than 50%, greater than 60%, greater than 70%, greater than 80%,greater than 90%, greater than 95%, greater than 96%, greater than 97%,greater than 98%, greater than 99%, or greater than 99.5% soluble withno precipitation observed at a concentration of greater than 0.001 g/L,0.005 g/L, 0.01 g/L, 0.05 g/L, 0.1 g/L, 0.2 g/L, 0.3 g/L, 0.4 g/L, 0.5g/L, 0.6 g/L, 0.7 g/L, 0.8 g/L, 0.9 g/L, 1 g/L, 5 g/L, 10 g/L, 20 g/L,30 g/L, 40 g/L, 50 g/L, 100 g/L, 200 g/L, 300 g/L, 400 g/L, 500 g/L, 600g/L, 700 g/L, 800 g/L, 900 g/L, 1000 g/L in deionized water, or in asuitable buffer such as, e.g., phosphate-buffered saline, pH 7.4 orsimilar physiological pH and at 20° C.

Sweetness

In some embodiments, the preparation of glycan therapeutics has adesired degree of sweetness. For example, sucrose (table sugar) is theprototype of a sweet substance. Sucrose in solution has a sweetnessperception rating of 1, and other substances are rated relative to this(e.g., fructose, is rated at 1.7 times the sweetness of sucrose). Insome embodiments, the sweetness of the preparation of glycantherapeutics ranges from 0.1 to 500,000 relative to sucrose. In someembodiments, the relative sweetness is 0.1, 0.2, 0.3, 0.4, 0.5, 0.6,0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 90, 100,150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800,850, 900, 950, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000,10000, 25000, 50000, 75000, 100000, 150000, 200000, 250000, 300000,350000, 40000, 450000, 500000, or more than 500,000 relative to sucrose(with sucrose scored as one). In some embodiments, the preparation ofglycan therapeutics is mildly sweet, or both sweet and bitter.

In some embodiments, the preparation of glycan therapeutics, e.g. apreparation that is substantially DP2+ or DP3+ (e.g. at least 80%, 90%,or at least 95%, or a fractionated preparation of DP2+ or DP3+), issubstantially imperceptible as sweet and the relative sweetness is about0, 0.0001, 0.001, 0.005, 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7,0.8, or about 0.9 relative to sucrose (with sucrose scored as one).

Identification and Characterization of Glycan Therapeutic Preparations

If desired, the glycan therapeutic preparations can be characterized byany method known in the art and by the methods described herein.

The molar percentage of species with a degree of polymerization (DP) ofn (denoted here as DP(n)) in a population is determined by highperformance liquid chromatography (HPLC), e.g., on an Agilent 1260Biolnert series instrument equipped with a refractive index (RI)detector and a variety of columns familiar to those skilled in the artusing water as the mobile phase. The columns are selected fromchemistries including HILIC, metal coordination, and aqueoussize-exclusion chromatography that best isolate the species of interest.Molar % DP(n) is determined by the formula:% DP(n)=100*AUC[DP(n)]/AUC[DP(total)],where AUC is defined as the area under the curve for the species ofinterest as determined by calibration to known standards. The molarpercentage of glycosidic bond isomers (% alpha and % beta) aredetermined by nuclear magnetic resonance (NMR) spectroscopy using avariety of 2D techniques familiar to those skilled in the art. Alpha-and beta-isomers may be distinguished, e.g., by their distinct shift onthe NMR spectrum and the molar percentage is determined by the formula:% (glycosidic isomer n) of glycosidic bonds=100*AUC[shift(isomern)]/AUC[shift(isomer alpha+isomer beta)],where AUC is defined as the area under the curve at a specific shiftvalue known to represent the desired isomer n. The molar percentage ofregiochemical isomers is determined in an analogous fashion using theformula:% (regioisomer n) of regioisomers=100*AUC[shift(regioisomern)]/AUC[shift(all regioisomers)].

The relative percentage of monomeric sugars making up the oligomericpopulation is determined, e.g., by total acidic digestion of theoligomeric sample followed by conversion to the alditol acetate followedby gas chromatographic (GC) analysis of the resultant monomericsolutions compared against GC of known standards. The molar percentageof monomer(n), where n can be any sugar, is determined by the formula:% (sugar n)=100*AUC[sugar n]/AUC[total of all monomeric sugars].

In some embodiments, the solubility of the preparation of glycantherapeutics can be controlled, e.g. by selecting the charge, structure(e.g. DP, degree of branching), and/or derivatization of the glycanunits.

For glycan therapeutic preparations, the monomeric building blocks (e.g.the monosaccharide or glycan unit composition), the anomericconfiguration of side chains, the presence and location of substituentgroups, degree of polymerization/molecular weight and the linkagepattern can be identified by standard methods known in the art, such as,e.g. methylation analysis, reductive cleavage, hydrolysis, GC-MS (gaschromatography-mass spectrometry), MALDI-MS (Matrix-assisted laserdesorption/ionization-mass spectrometry), ESI-MS (Electrosprayionization-mass spectrometry), HPLC (High-Performance Liquidchromatography with ultraviolet or refractive index detection),HPAEC-PAD (High-Performance Anion-Exchange chromatography with PulsedAmperometric Detection), CE (capillary electrophoresis), IR (infrared)/Raman spectroscopy, and NMR (Nuclear magnetic resonance)spectroscopy techniques. For polymers of crystalline consistency, thecrystal structure can be solved using, e.g., solid-state NMR, FT-IR(Fourier transform infrared spectroscopy), and WAXS (wide-angle X-rayscattering). The DP, DP distribution, and polydispersity can bedetermined by, e.g., viscosimetry and SEC (SEC-HPLC, high performancesize-exclusion chromatography). Alien groups, end groups andsubstituents can be identified, e.g., using SEC with labeling, aqueousanalytics, MALDI-MS, FT-IR, and NMR. To identify the monomericcomponents of the glycans methods such as, e.g. acid-catalyzedhydrolysis, HPLC (high performance liquid chromatography) or GLC(gas-liquid chromatography) (after conversion to alditol acetates) maybe used. To determine the linkages present in the glycans, in oneexample, the polysaccharide is methylated with methyl iodide and strongbase in DMSO, hydrolysis is performed, a reduction to partiallymethylated alditols is achieved, an acetylation to methylated alditolacetates is performed, and the analysis is carried out by GLC/MS(gas-liquid chromatography coupled with mass spectrometry). In someembodiments, to determine the polysaccharide sequence a partialdepolymerization is carried out using an acid or enzymes to determinethe structures. Possible structures of the polysaccharide are comparedto those of the hydrolytic oligomers, and it is determined which one ofthe possible structures could produce the oligomers. To identify theanomeric configuration, in one example, the intact polysaccharide or apreparation of oligosaccharides are subjected to enzymatic analysis,e.g. they are contacted with an enzyme that is specific for a particulartype of linkage, e.g., β-galactosidase, or α-glucosidase, etc., and NMRmay be used to analyze the products.

For example, the distribution of (or average) degree of polymerization(DP) of a glycan therapeutic preparation may be measured by injecting asample with a concentration of, e.g., 10-100 mg/mL onto an Agilent 1260BioPure HPLC (or similar) equipped with a 7.8×300 mm BioRad AminexHPX-42A column (or similar) and RI detector as described, e.g., in Gómezet al. (Purification, Characterization, and Prebiotic Properties ofPectic Oligosaccharides from Orange Peel Wastes, J Agric Food Chem,2014, 62:9769). Alternatively, a sample with a concentration may beinjected into a Dionex ICS5000 HPLC (or similar) equipped with a 4×250mm Dionex CarboPac PA1 column (or similar) and PAD detector asdescribed, e.g., in Holck et al., (Feruloylated and nonferuloylatedarabino-oligosaccharides from sugar beet pectin selectively stimulatethe growth of bifidobacterium spp. in human fecal in vitrofermentations, Journal of Agricultural and Food Chemistry, 2011, 59(12),6511-6519). Integration of the resulting spectrum compared against astandard solution of oligomers allows determination of the average DP.

Distribution of molecular weights can be measured, e.g, by MALDI massspectrometry. Oligosaccharide concentration can be measured with aMettler-Toledo sugar refractometer (or similar) with the final valueadjusted against a standardized curve to account for refractivedifferences between monomers and oligomers.

Distribution of glycoside regiochemistry can be characterized, e.g., bya variety of 2D-NMR techniques including COSY, HMBC, HSQC, DEPT, andTOCSY analysis using standard pulse sequences and a Bruker 500 MHzspectrometer. Peaks can be assigned by correlation to the spectra ofnaturally occurring polysaccharides with known regiochemistry.

In some embodiments, the relative peak assignment of a sample isdependent on a number of factors including the concentration and purityof the sample, the identity and quality of the solvent (e.g., theisotopically labeled solvent), and the pulse sequence utilized. As such,in embodiments, the relative peak assignment of, for example, a glycancomprising glucose may vary (e.g., by about 0.01 ppm, about 0.02 ppm, orabout 0.05 ppm) when the NMR spectrum is obtained in similar conditionsdue to said factors. In these instances as used herein, the terms“corresponding peak” or “corresponding peaks” refer to NMR peaksassociated with the same sample but that vary (e.g., by about 0.01 ppm,about 0.02 ppm, or about 0.05 ppm) due to factors including, forexample, the concentration and purity of the sample, the identity andquality of the isotopically labeled solvent, and the pulse sequenceutilized.

Monomeric compositions of oligomers may be measured, e.g., by thecomplete hydrolysis method in which a known amount of oligomer isdissolved into a strong acid at elevated temperature and allowedsufficient time for total hydrolysis to occur. The concentration ofindividual monomers may then be measured by the HPLC or GC methodsdescribed herein and known in the art to achieve relative abundancemeasurements as in Holck et al. Absolute amounts can be measured byspiking the HPLC sample with a known amount of detector active standardselected to prevent overlap with any of the critical signals.

The degree of branching in any given population may be measured by themethylation analysis method established, e.g, by Hakomori (J. Biochem.(Tokyo), 1964, 55, 205). With these data, identification of potentialrepeat units may be established by combining data from the totalhydrolysis, average DP, and methylation analysis and comparing themagainst the DEPT NMR spectrum. Correlation of the number of anomericcarbon signals to these data indicates if a regular repeat unit isrequired to satisfy the collected data as demonstrated, e.g., inHarding, et al. (Carbohydr. Res. 2005, 340, 1107).

Preparation of glycan therapeutics (e.g. those comprising monosaccharideor disaccharide glycan units such as glucose, galactose, fucose, xylose,arabinose, rhamnose, and mannose) may be identified using one, two,three, or four of the following parameters: a) the presence of 2, 3, 4,5, 6, 7 or more (e.g. at least 4 or 5) diagnostic anomeric NMR peakseach representing a different glycosidic bond type, b) an alpha- tobeta-bond ratio between about 0.8 to 1 and about 5 to 1 (e.g. betweenabout 1:1 and 4:1, commonly favoring the alpha bond type), c) at least 2or at least 3 different glycoside regiochemistries from the list of1,2-; 1,3-; 1,4-; and 1,6-substituted and at least 2 or at least 3different glycoside regiochemistries from list of 1,2,3-; 1,2,4-;1,2,6-; 1,3,4-; 1,3,6-; and 1,4,6-substituted, and d) a DP distributionin which at least 50%, 60%, 70% or at least 80% of the individualspecies have a DP of at least 2, at least 3, between 3 and 30 or between5 and 25. In some embodiments, glycan therapeutic preparations haveaverage properties (e.g., DP, DB, alpha:beta glycosidic bond ratio) thatare distinct from naturally occurring preparations of oligosaccharides.These structural features may be analyzed and optionally quantified byany suitable method known in the art and those described herein. Theglycan therapeutic preparations described herein have at least one, two,three, four, or at least five of the following characteristics:

-   -   (i) a distribution of molecular weights ranging, e.g. from about        DP3 to about DP30 or from about DP5 to about DP25 that may be        identified by quantitative mass spectrometry measurements,        SEC-HPLC, IAC-HPLC, or IEC-HPLC;    -   (ii) a significant proportion of both alpha and beta bonds, with        bond ratios, e.g., ranging from 0.8:1, 1:1, 2:1, 3:1, 4:1, to        5:1 (generally favoring the alpha stereochemistry) that may be        identified by a variety of NMR techniques including the HSQC        pulse sequence which allows explicit discrimination and        quantitation of signals from alpha and beta glycosides. The        presence of both alpha- and beta-glycosidic bonds in the        observed ratios (see Table 6, showing the presence of a large        proportion of both alpha and beta bonds across the single and        multi-sugar glycans tested) in glycan therapeutic preparation of        some embodiments, is distinct from preparations of naturally        occurring oligo- or polysaccharides which generally favor one        primary glycosidic stereochemistry and optionally comprise only        a relatively small portion of the opposing stereochemistry;    -   (iii) presence of at least one, two, three or four glycoside        regiochemistries that may be identified either by a fingerprint        NMR process or by the permethylation branching identification        developed by Hakomori, et al. In some embodiments, glycan        therapeutic preparations have at least 0.1%, 0.2%, 0.5%, 1%, 2%,        3%, 4%, 5%, 6%, 7%, 8%, 9%, or at least 10% of one, two, three        or four of the 1,2-; 1,3-; 1,4-, and 1,6-glycoside bond types.        In some embodiments, glycan therapeutic preparations have at        least 0.1%, 0.2%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, or        at least 10% of two of the 1,2-; 1,3-; 1,4-, and 1,6-glycoside        bond types. In some embodiments, glycan therapeutic preparations        have at least 0.1%, 0.2%, 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%,        9%, or at least 10% of three of the 1,2-; 1,3-; 1,4-, and        1,6-glycoside bond types. In some embodiments, glycan        therapeutic preparations have at least 0.1%, 0.2%, 0.5%, 1%, 2%,        3%, 4%, 5%, 6%, 7%, 8%, 9%, or at least 10% of all four of the        1,2-; 1,3-; 1,4-, and 1,6-glycoside bond types. In some        embodiments, the glycan therapeutic preparation additionally        comprises at least 0.1%, 0.2%, 0.5%, 1%, 2%, 3%, 4% or at least        5% of branched bond types. In some embodiments, the glycan        therapeutic preparation comprises at least 0.1%, 0.2%, 0.5%, 1%,        2%, 3%, 4% or at least 5% of at least one, two, or at least        three branched bond types including 1,3,6-; 1,4,6-; or        1,2,4-glycosides. In some embodiments, the glycan therapeutic        preparation comprises at least two branched bond types of        1,3,6-; 1,4,6-; or 1,2,4-glycosides. In some embodiments, the        glycan therapeutic preparation comprises at least 0.1%, 0.2%,        0.5%, 1%, 2%, 3%, 4% or at least 5% of three branched bond types        of 1,3,6-; 1,4,6-; or 1,2,4-glycosides. Sugars that do not have        a hydroxyl group at a given position X will not will not have        the 1,X-bond type, e.g. fucose (6-dehydroxy-galactose) will not        have 1,6-glycosidic bonds but will have 1,2-; 1,3-; and        1,4-glycosidic bonds. In some embodiments, the glycan        therapeutic preparation comprises at least 0.1%, 02%, 0.5%, 1%,        2%, or at least 3% of monomeric glycan units in furanose form.        The presence of a large number of glycoside regiochemistries and        branching (see FIG. 4 for 3 exemplary glycans) in glycan        therapeutic preparation of some embodiments, is distinct from        preparations of naturally occurring oligo- or polysaccharides        which generally favor specific bond architectures. Although all        of these regiochemistries are known to occur in oligosaccharides        of natural sources, preparations of naturally sourced        oligosaccharide do not comprise the number and complexity of        regiochemistries that are exhibited by glycan therapeutic        preparations of some embodiments.    -   (iv) a distribution of glycosidic bonds that represents at least        50%, 60%, 70%, 80% or at least 90% of all possible combinations        of regio- and stereochemistries. Individually, the regiochemical        distribution can be determined by branching analysis and the        stereochemical distribution can be determined by NMR. The        HSQC-NMR. In some embodiments, the glycan therapeutic        preparations exhibit a diversity of peaks in the anomeric region        that are associated with a multiplicative combination of both        regiochemistry and stereochemistry. In some embodiments, the        glycan therapeutic preparation comprises at least two or at        least three of alpha-1,2-; alpha-1,3-; alpha-1,4-; and        alpha-1,6-glycosides and at least two, or at least three of        beta-1,2-; beta-1,3-; beta-1,4-; and beta-1,6-glycosides. In        some embodiments, the glycan therapeutic preparation comprises        all four of alpha-1,2-; alpha-1,3-; alpha-1,4-; and        alpha-1,6-glycosides and all four of beta-1,2-; beta-1,3-;        beta-1,4-; and beta-1,6-glycosides. As an exemplar, HSQC of a        glu100 preparation shows that the preparation contains all        alpha-1,2-; alpha-1,3-; alpha-1,4-; and alpha-1,6-glycosides as        well as all beta-1,2-; beta-1,3-; beta-1,4-; and        beta-1,6-glycosides. Sugars that do not have a hydroxyl group at        a given position X will not will not have the 1,X-bond type,        e.g. fucose (6-dehydroxy-galactose) will not have 1,6-glycosidic        bonds but will have 1,2-; 1,3-; and 1,4-glycosidic bonds;    -   (v) a unique HSQC “fingerprint” that is the result of the        additive nature of the HSQC pulse sequence. For any given        glycan, the HSQC spectra allow the identification of peaks that        are unique to specific regio- and stereochemical bond        arrangement. For example, FIG. 5 shows a partial assignment of        the spectra of a glu100 preparation demonstrating how these        peaks may be used to identify specific glycosidic regio- and        stereochemistries. Component glycan units (e.g. sugars) within a        glycan demonstrate spin-isolation in the HSQC pulse sequence and        the HSQC spectrum of any glycan consisting of multiple sugars is        the sum of peaks of its individual sugars. Glycan unit        constituents (e.g. monomers) can be identified by an HSQC        spectrum that shows 4, 5, 6 or more of the peaks listed in Table        7 for each of its component glycan units (e.g. sugars). The        spectra in FIGS. 3 a-c exemplify this by comparing the spectra        of preparations of glu100, gal100, and glu50gal50.        Pharmaceutical Compositions, Medical Foods, Supplements, and        Unit Dosage Forms

Provided herein are pharmaceutical compositions comprising glycantherapeutic preparations. Further provided herein are medical foodscomprising glycan therapeutic preparations. Still further providedherein are dietary supplements comprising glycan therapeuticpreparations. Optionally, the pharmaceutical compositions, medical foodsand dietary supplements comprising glycan therapeutic preparationsfurther comprise a second (or third, fourth, etc.) therapeutic agent oractive compound. In one embodiment, the agent or compound is a prebioticsubstance, such as a dietary fiber. In one embodiment, the agent orcompound is a probiotic bacterium. In one embodiment, the agent orcompound is a micronutrient, such as a vitamin, mineral or polyphenolcompound. In one embodiment, the agent or compound is a therapeuticdrug, such as, e.g., an anti-cancer drug, a pain management drug, a drugthat manages treatment side-effects, a drug that manages metabolism, ananti-inflammatory drug, or an anti-microbial agent.

In some embodiments, the pharmaceutical compositions and medical foodsand dietary supplements comprising glycan therapeutic preparations donot contain a prebiotic substance. In some embodiments, thepharmaceutical compositions and medical foods and dietary supplementscomprising glycan therapeutic preparations do not contain a probioticbacterium.

In some embodiments, the pharmaceutical compositions or medical foodsand dietary supplements comprise a glycan therapeutic preparation ofxyl100, rha100, ara100, gal100, glu100, fuc100, fru100 or man100.

In some embodiments, the pharmaceutical compositions or medical foodsand dietary supplements comprise a glycan therapeutic preparation ofara50gal50, xyl75gal25, ara80xyl20, ara60xyl40, ara50xyl50, glu80man20,glu60man40, man60glu40, man80glu20, gal75xyl25, glu50gal50, man62glu38,and the hybrid glycans glu90sor10 or glu90gly10.

In some embodiments, the pharmaceutical compositions or medical foodsand dietary supplements comprise a glycan therapeutic preparation ofxyl75glu12gal12, xyl33glu33gal33, glu33gal33fuc33, man52glu29gal19, andthe hybrid glycan glu33gal33neu33.

In some embodiments, the pharmaceutical compositions or medical foodsand dietary supplements comprise a glycan therapeutic preparation ofglu100, ara100, xyl100, glu50gal50, man52glu29gal19, or glu33gal33fuc33.

In some embodiments, the pharmaceutical compositions or medical foodsand dietary supplements comprise a glycan therapeutic preparation ofglu100 and man52glu29gal19.

In some embodiments, the pharmaceutical compositions or medical foodsand dietary supplements comprise a glycan therapeutic preparation ofman100.

In some embodiments, the pharmaceutical compositions or medical foodsand dietary supplements comprise a glycan therapeutic preparation ofxyl100.

In some embodiments, pharmaceutical compositions and medical foods anddietary supplements comprising glycan therapeutic preparations (and kitscomprising same) comprise one or more micronutrient. In someembodiments, the micronutrient is selected from the group consisting ofa trace mineral, choline, a vitamin, and a polyphenol.

In some embodiments, the micronutrient is a trace metal. Trace mineralssuitable as a micronutrient include boron, cobalt, chromium, calcium,copper, fluoride, iodine, iron, magnesium, manganese, molybdenum,selenium, and zinc.

In some embodiments, the micronutrient is a vitamin. Vitamins suitableas a micronutrient include Vitamin B complex, Vitamin B1 (thiamin),Vitamin B2 (riboflavin), Vitamin B3 (niacin), Vitamin B5 (pantothenicacid), Vitamin B6 group (pyridoxine, pyridoxal, pyridoxamine), VitaminB7 (biotin), Vitamin B8 (ergadenylic acid), Vitamin B9 (folic acid),Vitamin B12 (cyanocobalamin), Choline, Vitamin A (retinol), Vitamin C(ascorbic acid), Vitamin D, Vitamin E (tocopherol), Vitamin K,carotenoids (alpha carotene, beta carotene, cryptoxanthin, lutein,lycopene) and zeaxanthin.

In some embodiments, the micronutrient is a polyphenol. Polyphenols arechemical compounds or molecules that are characterized by having atleast one aromatic ring with one or more hydroxyl groups. In someembodiments, the polyphenol is a synthetic polyphenol or a naturallyoccurring polyphenol. In some embodiments, the polyphenol is a naturallyoccurring polyphenol and is derived from plant source material.

In some embodiments, the polyphenol is a flavonoid or catechin. In someembodiments, the flavonoid or catechin is selected from anthocyanins,chalcones, dihydrochalcones, dihydroflavonols, flavanols, flavanones,flavones, flavonols and isoflavonoids. In some embodiments, thepolyphenol is a lignan.

In some embodiments, the polyphenol is selected fromalkylmethoxyphenols, alkylphenols, curcuminoids, furanocoumarins,hydroxybenzaldehydes, hydroxybenzoketones, hydroxycinnamaldehydes,hydroxycoumarins, hydroxyphenylpropenes, methoxyphenols, naphtoquinones,phenolic terpenes, and tyrosols. In some embodiments, the polyphenol isa tannin or tannic acid.

In some embodiments, the polyphenol is selected from hydroxybenzoicacids, hydroxycinnamic acids, hydroxyphenylacetic acids,hydroxyphenylpropanoic acids, and hydroxyphenylpentanoic acids. In someembodiments, the polyphenol is a stilbene.

In some embodiments, the pharmaceutical compositions and medical foodsand dietary supplements comprising glycan therapeutic preparationsdescribed herein further comprise a prebiotic substance or preparationthereof.

Prebiotics include various galactans and carbohydrate based gums, suchas psyllium, guar, carrageen, gellan, lactulose, and konjac. In someembodiments, the prebiotic is one or more of galactooligosaccharides(GOS), lactulose, raffinose, stachyose, lactosucrose,fructo-oligosaccharides (FOS, e.g. oligofructose or oligofructan),inulin, isomalto-oligosaccharide, xylo-oligosaccharides (XOS),paratinose oligosaccharide, isomaltose oligosaccharides (IMOS),transgalactosylated oligosaccharides (e.g.transgalacto-oligosaccharides), transgalactosylate disaccharides,soybean oligosaccharides (e.g. soyoligosaccharides), chitosanoligosaccharide (chioses), gentiooligosaccharides, soy- andpectin-oligosaccharides, glucooligosaccharides, pecticoligosaccharides,palatinose polycondensates, difructose anhydride III, sorbitol,maltitol, lactitol, polyols, polydextrose, linear and branched dextrans,pullalan, hemicelluloses, reduced paratinose, cellulose, beta-glucose,beta-galactose, beta-fructose, verbascose, galactinol, xylan, inulin,chitosan, beta-glucan, guar gum, gum arabic, pectin, high sodiumalginate, and lambda carrageenan, or mixtures thereof.

In some embodiments, the pharmaceutical compositions and medical foodsand dietary supplements comprising glycan therapeutic preparationsfurther comprise a probiotic bacterium or preparation thereof, e.g.,derived from bacterial cultures that are generally recognized as safe(GRAS) or known commensal or probiotic microbes.

Examples of suitable probiotics include organisms classified as generaBacteroides, Blautia, Clostridium, Fusobacterium, Eubacterium,Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia,Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacillus,Bacillus, Enterococcus, Escherichia, Streptococcus, Saccharomyces,Streptomyces, and family Christensenellaceae. Non-exclusive examples ofprobiotic bacteria that can be used in the methods and compositionsdescribed herein include L. acidophilus, Lactobacillus species, such asL. crispatus, L. casei, L. rhamnosus, L. reuteri, L. fermentum, L.plantarum, L. sporogenes, and L. bulgaricus, as well as Bifidobacterumspecies, such as B. lactis, B. animalis, B. bifidum, B. longum, B.adolescentis, and B. infantis. Yeasts, such as Saccharomyces boulardii,are also suitable as probiotics for administration to the gut, e.g. viaoral dosage forms or foods. For example, yogurt is a product whichalready contains bacteria species, such as Lactobacillus bulgaricus andStreptococcus thermophilus.

Beneficial bacteria may include one or more of the genus Akkermansia,Anaerofilum, Bacteroides, Blautia, Bifidobacterium, Butyrivibrio,Clostridium, Coprococcus, Dialister, Dorea, Fusobacterium, Eubacterium,Faecalibacterium, Lachnospira, Lactobacillus, Phascolarctobacterium,Peptococcus, Peptostreptococcus, Prevotella, Roseburia, Ruminococcus,and Streptococcus, and/or one or more of the species Akkermansiamuniciphilia, minuta, Clostridium coccoides, Clostridium leptum,Clostridium scindens, Dialister invisus, Eubacterium rectal, Eubacteriumeligens, Faecalibacterium prausnitzii, Streptococcus salivarius, andStreptococcus thermophilus. In some embodiments, the probiotic orcommensal bacteria include one or more of the bacteria listed in Tables1, 3, and 4.

Beneficial bacteria for the modulation of the gastrointestinalmicrobiota may include bacteria that produce organic acids (e.g. SCFAs)or that produce cytotoxic or cytostatic agents (to inhibit pathogenicgrowth), such as, e.g., hydrogen peroxide (H₂O₂) and bacteriocins.Bacteriocins are small antimicrobial peptides which can kill bothclosely-related bacteria, or exhibit a broader spectrum of activity(e.g., nisin).

The prebiotic substances and probiotic strains that may be combined withglycan therapeutics described herein to produce a composition may beisolated at any level of purity by standard methods and purification canbe achieved by conventional means known to those skilled in the art,such as distillation, recrystallization and chromatography. If desired,the cultivated bacteria may be used in the composition. The bacteria maybe separated from the culture broth by any method including, withoutlimitations, centrifugation, filtration or decantation. The cellsseparated from the fermentation broth are optionally washed by water,saline (0.9% NaCl) or with any suitable buffer. The wet cell massobtained may be dried by any suitable method, e.g., by lyophilization.

In some embodiments, the probiotic bacteria are lyophilized vegetativecells. In some embodiments, preparations of spores from sporulatingprobiotic bacteria are used.

In one embodiment, the pharmaceutical compositions, medical foods, ordietary supplements comprise a glycan therapeutic preparation andprobiotics whose viability has been partially attenuated (e.g. a mixturecomprising 10%, 20%, 30%, 40%, 50% or more non-viable bacteria), orprobiotics consisting primarily of non-viable microbes (e.g. 95%, 96%,97%, 98%, 99%, 99.9% or 100%). The compositions may further comprisemicrobial membranes and/or cell walls that have been isolated andpurified from microbes or microbial vesicles. If desired, the probioticorganism(s) can be incorporated into the pharmaceutical glycantherapeutic composition as a culture in water or another liquid orsemisolid medium in which the probiotic remains viable. In anothertechnique, a freeze-dried powder containing the probiotic organism maybe incorporated into a particulate material or liquid or semisolidmaterial comprising the glycan preparation by mixing or blending.

In some embodiments, the pharmaceutical compositions and medical foodsand dietary supplements comprising glycan therapeutic preparationsfurther comprise a second therapeutic agent or preparation thereof, suchas a drug.

For example, the second therapeutic agent is an anti-cancer drug.Examples of anti-cancer drugs include: checkpoint inhibitors (such as,e.g., anti-PD-1, anti-PD-L1, anti-CTLA4, anti-TIM-3, anti-LAG-3);vaccines (such as, e.g., autologous cancer vaccines, allogeneic cancervaccines, neoantigen cancer vaccines, shared antigen cancer vaccines(e.g. NY-ESO-1)); targeted kinase inhibitors (such as, e.g., Imatinibmesylate, Ibrutinib, Neratinib, Palpociclib, Erlotinib, Lapatinib);antibodies (such as, e.g., Bevacizumab, Trastuzumab, Rituximab,Cetuximab); chemotherapeutics (such as, e.g., irinotecan, 5-flurouracil,lenalidomide, capecitabine, docetaxel), antibody-drug conjugates (e.g.ado-trastuzumab emtansine), and any other anti-cancer drug mentionedelsewhere herein.

For example, the second therapeutic agent is a pain-management drug. Insome embodiments, the pain-management drug is an opioid, such as, e.g.,codeine, fentanyl, hydrocodone, hydrocodone/acetaminophen,hydromorphone, meperidine, methadone, morphine, oxycodone, oxycodone andacetaminophen, or oxycodone and naloxone. In other embodiments, thepain-management drug is a non-opioid, such as, e.g., acetaminophen ornonsteroidal anti-inflammatory drugs (NSAIDs), such as aspirin andibuprofen.

For example, the second therapeutic agent is an antidepressant, such as,e.g., amitriptyline, imipramine, doxepin and trazodone.

For example, the second therapeutic agent is an antiepileptic, such as,e.g., gabapentin.

For example, the second therapeutic agent is a steroid, such as, e.g.prednisone or dexamethasone.

In some embodiments, the second therapeutic agent is a drug for managinga GI tract motility disorder, such as, e.g., acute diarrhea, chronicdiarrhea, acute constipation, or chronic constipation. Drugs for GImotility disorders include opioids, antibiotics, bile acid sequestrantsand heavy metal containing compounds (bismuth subsalicylate). Drugs tomanage diarrhea include, but are not limited to liperamide,diphenoxylate with atropine, Cholestyramine, and bismuth subsalicylate.Drugs to manage constipation include, but are not limited to magnesiumcitrate, magnesium hydroxide, magnesium sulfate/potassium sulfate/sodiumsulfate, sodium biphosphate/sodium phosphate, lactulose, sennosides,bisacodyl, polyethylene glycol (e.g., PEG3350), docusate, polycarbophil,psyllium, methylcellulose, and mineral oil.

In some embodiments, the therapeutic agent is an anti-inflammatoryagent, such as, e.g., an NSAID, including ibuprofen, naproxen sodium,aspirin, celecoxib, sulindac, oxaprozin, salsalate, diflunisal,piroxicam, indomethacin, etodolac, meloxicam, nabumetone, ketorolactromethamine, naproxen/esomeprazole, or diclofenac.

In some embodiments, the second therapeutic agent is an antimicrobialagent, such as an antibiotic, an antifungal agent, or an antiviral.Antibiotics include aminoglycosides, such as amikacin, gentamicin,kanamycin, neomycin, streptomycin, and tobramycin; cephalosporins, suchas cefamandole, cefazolin, cephalexin, cephaloglycin, cephaloridine,cephalothin, cephapirin, and cephradine; macrolides, such aserythromycin and troleandomycin; penicillins, such as penicillin G,amoxicillin, ampicillin, carbenicillin, cloxacillin, dicloxacillin,methicillin, nafcillin, oxacillin, phenethicillin, and ticarcillin;polypeptide antibiotics, such as bacitracin, colistimethate, colistin,polymyxin B; tetracyclines, such as chlortetracycline, demeclocycline,doxycycline, methacycline, minocycline, tetracycline, andoxytetracycline; and miscellaneous antibiotics such as chloramphenicol,clindamycin, cycloserine, lincomycin, rifampin, spectinomycin,vancomycin, viomycin and metronidazole.

The glycan therapeutic preparations described herein and the therapeuticagent or active compound may be comingled or mixed in a singlepharmaceutical composition or medical food or dietary supplement. Inother embodiments, they may be contained in separate containers (and/orin various suitable unit dosage forms) but packaged together in one ormore kits. In some embodiments, the preparations or compositions are notpackaged or placed together.

In some embodiments, a pharmaceutical composition comprises between 0.1%and 100% glycan therapeutic preparation by w/w, w/v, v/v or molar %. Inanother embodiment, a pharmaceutical composition comprises about 1%, 2%,3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%,19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%,33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%,47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%,61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%,75%, 76%, 77%, 78%, 79% 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%,89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% ofglycan therapeutic preparation by w/w, w/v, v/v or molar %. In oneembodiment, a pharmaceutical composition comprises about 1-90%, about10-90%, about 20-90%, about 30-90%, about 40-90%, about 40-80%, about40-70%, about 40-60%, about 40-50%, about 50-90%, about 50-80%, about50-70%, about 50-60%, about 60-90%, about 60-80%, about 60-70%, about70-90%, about 70-80%, about 70-90%, about 70-80%, about 80-90%, about90-96%, about 93-96%, about 93-95%, about 94-98%, about 93-99%, or about90-100% of glycan therapeutic preparation by w/w, w/v, v/v or molar %.

Optionally, the pharmaceutical compositions and medical foods anddietary supplements comprising glycan therapeutic preparations compriseone or more excipients or carriers, including diluents, binders,disintegrants, dispersants, lubricants, glidants, stabilizers,surfactants, flavoring agents, and colorants. The pharmaceuticalcomposition can comprise from about 1% to about 90% of the one or moreexcipients or carriers by w/w, w/v, v/v or molar %. For example, thepharmaceutical composition can comprise about 1-90%, 1-75%, 1-60%,1-55%, 1-50%, 1-45%, 1-40%, 1-25%, 1-15%, 1-10%, 10-90%, 10-75%, 10-60%,10-55%, 10-50%, 10-45%, 10-40%, 10-25%, 10-15%, 15-90%, 15-75%, 15-60%,15-55%, 15-50%, 15-45%, 15-40%, 15-25%, 25-90%, 25-75%, 25-60%, 25-55%,25-50%, 25-45%, 25-40%, 40-90%, 40-75%, 40-60%, 40-55%, 40-50%, 40-45%,45-90%, 45-75%, 45-60%, 45-55%, 45-50%, 50-90%, 50-75%, 50-60%, 50-55%,55-90%, 55-75%, 55-60%, 60-90%, 60-75%, 75-90% of the one or moreexcipients or carriers by w/w, w/v, v/v or molar %.

Pharmaceutical carriers or vehicles suitable for administration of thepharmaceutical glycan therapeutic compositions provided herein includeall such carriers known to those skilled in the art to be suitable forthe particular mode of administration. In addition, the compositions canone or more components that do not impair the desired action, or withcomponents that supplement the desired action, or have another action.

Dosage Forms

The glycan therapeutic preparations described herein may be formulatedinto any suitable dosage form, e.g. for oral or enteral administrationor formulated for injection. The dosage forms described herein can bemanufactured using processes that are known to those of skill in theart. The dosage form may be suitable for any route of administration,including orally or parenterally, such as intravenously,intramuscularly, subcutaneously, intraorbitally, intracapsularly,intraperitoneally, intrarectally, intracisternally, intratumorally,intravasally, intradermally or by passive or facilitated absorptionthrough the skin.

The dosage form may be a packet, such as any individual container thatcontains a pharmaceutical glycan therapeutic composition in the form of,e.g., a liquid (wash/rinse), a gel, a cream, an ointment, a powder, atablet, a pill, a capsule, a depository, a single-use applicator ormedical device (e.g. a syringe). For example, provided is also anarticle of manufacture, such as a container comprising a unit dosageform of the pharmaceutical glycan therapeutic composition, and a labelcontaining instructions for use of such glycan therapeutic.

Forms of the compositions that can be used orally include tablets,push-fit capsules made of gelatin, as well as soft, sealed capsules madeof gelatin and a plasticizer, such as glycerol or sorbitol. Tablets canbe made by compression or molding, optionally with one or more accessoryingredients. Compressed tablets can be prepared by compressing in asuitable machine the active ingredient in a free-flowing form such as apowder or granules, optionally mixed with binders (e.g., povidone,gelatin, hydroxypropylmethyl cellulose), inert diluents, preservative,antioxidant, disintegrant (e.g., sodium starch glycolate, cross-linkedpovidone, cross-linked sodium carboxymethyl cellulose) or lubricating,surface active or dispersing agents. Molded tablets can be made bymolding in a suitable machine a mixture of the powdered compoundmoistened with an inert liquid diluent. The tablets can optionally becoated or scored and can be formulated so as to provide slow orcontrolled release of the active ingredient therein. Tablets canoptionally be provided with an enteric coating, to provide release inparts of the gut (e.g., colon, lower intestine) other than the stomach.All formulations for oral administration can be in dosages suitable forsuch administration. The push-fit capsules can contain the activeingredients in admixture with filler such as lactose, binders such asstarches, and/or lubricants such as talc or magnesium stearate and,optionally, stabilizers. In soft capsules, the active compounds and/orother agents (e.g., prebiotics or probiotics) can be dissolved orsuspended in suitable liquids, such as fatty oils, liquid paraffin, orliquid polyethylene glycols. In addition, stabilizers can be added.Dragee cores are provided with suitable coatings. For this purpose,concentrated sugar solutions can be used, which can optionally containgum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethyleneglycol, or titanium dioxide, lacquer solutions, and suitable organicsolvents or solvent mixtures. Dyestuffs or pigments can be added to thetablets or Dragee coatings for identification or to characterizedifferent combinations of active compound doses.

Formulations for oral use can also be presented as hard gelatin capsuleswherein the active ingredient is mixed with an inert solid diluent, forexample, calcium carbonate, calcium phosphate or kaolin, or as softgelatin capsules wherein the active ingredient is mixed with watersoluble carrier such as polyethylene glycol or an oil medium, forexample peanut oil, liquid paraffin, or olive oil.

In one embodiment, a provided glycan therapeutic composition includes asoftgel formulation. A softgel can contain a gelatin based shell thatsurrounds a liquid fill. The shell can be made of gelatin, plasticizer(e.g., glycerin and/or sorbitol), modifier, water, color, antioxidant,or flavor. The shell can be made with starch or carrageenan. The outerlayer can be enteric coated. In one embodiment, a softgel formulationcan include a water or oil soluble fill solution, or suspension of acomposition covered by a layer of gelatin.

Formulations for oral use may also be presented in a liquid dosage from.Liquid preparations can be in the form of, for example, aqueous or oilysuspensions, solutions, emulsions syrups or elixirs, or can be presentedas a dry product for reconstitution with water or other suitable vehiclebefore use. Such liquid preparations can contain conventional additives,such as suspending agents, for example sorbitol, methyl cellulose,glucose syrup, gelatin, hydroxyethyl cellulose, carboxymethyl cellulose,aluminum stearate gel or hydrogenated edible fats, emulsifying agents,for example lecithin, sorbitan monooleate, acacia; nonaqueous vehicles(which can include edible oils), for example almond oil, oily esterssuch as glycerine, propylene glycol, or ethyl alcohol; preservatives,for example methyl or propyl p-hydoxybenzoate or sorbic acid, and, ifdesired, conventional flavoring or coloring agents. In some embodiments,liquid formulations can comprise, for example, an agent inwater-in-solution and/or suspension form; and a vehicle comprisingpolyethoxylated castor oil, alcohol, and/or a polyoxyethylated sorbitanmono-oleate with or without flavoring. Each dosage form may comprise aneffective amount of a glycan therapeutic and can optionally comprisepharmaceutically inert agents, such as conventional excipients,vehicles, fillers, binders, disintegrants, pH adjusting substances,buffer, solvents, solubilizing agents, sweeteners, coloring agents, andany other inactive agents that can be included in pharmaceutical dosageforms for administration. Examples of such vehicles and additives can befound in Remington's Pharmaceutical Sciences, 22nd edition (2012).

The pharmaceutical compositions provided herein can be in unit-dosageforms or multiple-dosage forms. A unit-dosage form, as used herein,refers to physically discrete unit suitable for administration to humanin need thereof. In an embodiment, the unit-dosage form is provided in apackage. Each unit-dose can contain a predetermined quantity of anactive ingredient(s) sufficient to produce the desired therapeuticeffect, in association with other pharmaceutical carriers or excipients.Examples of unit-dosage forms include ampoules, syringes, andindividually packaged tablets and capsules. Unit-dosage forms can beadministered in fractions or multiples thereof. A multiple-dosage formis a plurality of identical unit-dosage forms packaged in a singlecontainer, which can be administered in segregated unit-dosage form.Examples of multiple-dosage forms include vials, bottles of tablets orcapsules, or bottles of pints or gallons. In another embodiment themultiple dosage forms comprise different pharmaceutically active agents.For example a multiple dosage form can be provided which comprises afirst dosage element comprising a composition comprising a glycantherapeutic and a second dosage element comprising a second activecompound or therapeutic agent (e.g. an anti-cancer drug). The dosageelements can be in a modified release form. In this example, a pair ofdosage elements can make a single unit dosage. In one embodiment, a kitis provided comprising multiple unit dosages, wherein each unitcomprises a first dosage element comprising a composition comprising aglycan therapeutic and a second dosage element comprising a secondactive compound or therapeutic agent (e.g., a pharmaceutical agent, aprobiotic, a prebiotic, a micronutrient, etc. or a combination thereof).

In some embodiments, the unit-dosage form comprises between about 0.001mg to about 10 g of the glycan therapeutic. For example, the unit-dosageform may comprise about 0.001 mg to about 9.5 g, about 0.005 mg to about9 g, about 0.01 mg to about 8.5 g, about 0.05 mg to about 8 g, about0.075 mg to about 7.5 g, about 0.1 mg to about 7 g, about 0.25 mg toabout 6.5 g, about 0.5 mg to about 6 g, about 0.75 mg to about 5.5 g,about 1 mg to about 5 g, about 2.5 mg to about 4.5 g, about 5 mg toabout 4 g, about 7.5 mg to about 3.5 g, about 10 mg to about 3 g, about12.5 mg to about 2.5 g, about 15 mg to about 2 g, about 17.5 mg to about1.5 g, about 20 mg to about 1 g, about 25 mg to about 750 mg, about 50mg to about 500 g, or about 75 mg to about 250 mg of the glycantherapeutic.

In certain embodiments, the unit-dosage form may comprise about 1 g toabout 5 g, about 1 g to about 10 g, about 1 g to about 15 g, about 1 gto about 20 g, about 1 g to about 25 g, about 1 g to about 30 g, about 5g to about 10 g, about 5 g to about 15 g, about 5 g to about 20 g, about5 g to about 25 g, about 5 g to about 30 g, about 10 g to about 20 g, orabout 10 g to about 30 g of the glycan therapeutic.

In certain embodiments, the unit-dosage form comprises about 0.001 mg toabout 100 mg, about 0.005 mg to about 75 mg, about 0.01 mg to about 50mg, about 0.05 mg to about 25 mg, about 0.1 mg to about 10 mg, about 0.5mg to about 7.5 mg, or about 1 mg to about 5 mg of the glycantherapeutic. In other embodiments, the unit-dosage form comprises about1 mg to about 100 mg, about 2.5 mg to about 75 mg, about 5 mg to about50 mg, or about 10 mg to about 25 mg of the glycan therapeutic. In otherembodiments, the unit-dosage form comprises about 100 mg to about 10 g,about 250 mg to about 7.5 g, about 500 mg to about 5 g, about 750 mg toabout 2.5 g, or about 1 g to about 2 g of the glycan therapeutic.

In other embodiments, the unit-dosage form comprises between about 0.001mL to about 1000 mL of the glycan therapeutic. For example, theunit-dosage form may comprise about 0.001 mL to about 950 mL, about0.005 mL to about 900 mL, about 0.01 mL to about 850 mL, about 0.05 mLto about 800 mL, about 0.075 mL to about 750 mL, about 0.1 mL to about700 mL, about 0.25 mL to about 650 mL, about 0.5 mL to about 600 mL,about 0.75 mL to about 550 mL, about 1 mL to about 500 mL, about 2.5 mLto about 450 mL, about 5 mL to about 400 mL, about 7.5 mL to about 350mL, about 10 mL to about 300 mL, about 12.5 mL to about 250 mL, about 15mL to about 200 mL, about 17.5 mL to about 150 mL, about 20 mL to about100 mL, or about 25 mL to about 75 mL of the glycan therapeutic.

In certain embodiments, the unit-dosage form comprises about 0.001 mL toabout 10 mL, about 0.005 mL to about 7.5 mL, about 0.01 mL to about 5mL, about 0.05 mL to about 2.5 mL, about 0.1 mL to about 1 mL, about0.25 mL to about 1 mL, or about 0.5 mL to about 1 mL of the glycantherapeutic. In other embodiments, the unit-dosage form comprises about0.01 mL to about 10 mL, about 0.025 mL to about 7.5 mL, about 0.05 mL toabout 5 mL, or about 0.1 mL to about 2.5 mL of the glycan therapeutic.In other embodiments, the unit-dosage form comprises about 0.1 mL toabout 10 mL, about 0.25 mL to about 7.5 mL, about 0.5 mL to about 5 mL,about 0.5 mL to about 2.5 mL, or about 0.5 mL to about 1 mL of theglycan therapeutic.

In some embodiments, the unit-dosage form, e.g., a tablet, capsule(e.g., a hard capsule, push-fit capsule, or soft capsule), or softgel,has a body length of between about 0.1 inches to about 1.5 inches (e.g.,about 0.5 inches and about 1 inch), or about 5 mm to about 50 mm (e.g.,about 10 mm to about 25 mm). In some embodiments, the unit-dosage form.e.g., a tablet, capsule (e.g., a hard capsule, push-fit capsule, or softcapsule), or softgel, has an external diameter of about 0.05 inches toabout 1 inch (e.g., about 0.1 inches to about 0.5 inches), or about 1 mmto about 25 mm (e.g., about 5 mm to about 10 mm).

Each unit-dosage form of the glycan therapeutic may have a caloric valueof between about 0.01 kcal and about 1000 kcal. For example, theunit-dosage form may have a caloric value of about 0.01 kcal to about900 kcal, about 0.05 kcal to about 800 kcal, about 0.1 kcal to about 700kcal, about 0.25 kcal to about 600 kcal, about 0.5 kcal to about 500kcal, about 0.75 kcal to about 400 kcal, about 1 kcal to 300 kcal, about5 kcal to about 200 kcal, or about 10 kcal to about 100 kcal. In certainembodiments, the unit-dosage form of the glycan therapeutic has acaloric value of between 10 kcal to about 500 kcal. In otherembodiments, the unit-dosage form of the glycan therapeutic has acaloric value of between 50 kcal to about 500 kcal.

In still other embodiments, the unit-dosage form may have a caloricvalue of about 0.001 kcal to about 100 kcal, about 0.005 kcal to about90 kcal, about 0.01 kcal to about 80 kcal, about 0.025 kcal to about 70kcal, about 0.05 kcal to about 60 kcal, about 0.075 kcal to about 50kcal, about 0.1 kcal to 40 kcal, about 0.25 kcal to about 30 kcal, about0.5 kcal to about 25 kcal, about 0.25 kcal to about 20 kcal, or about0.1 kcal to about 10 kcal.

The unit-dosage form of the glycan therapeutic may be formulated todissolve in an aqueous solution (e.g., water, milk, juice, and the like)and is orally administered as a beverage, syrup, solution, orsuspension. For example, the unit-form dosage of the glycan therapeuticmay comprise a cube, packet, lozenge, pill, tablet, capsule, candy,powder, elixir, or concentrated syrup formulated for dissolving into anaqueous solution prior to oral administration. In other embodiments, theunit-dosage form of the glycan therapeutic may comprise a cube, packet,lozenge, pill, tablet, capsule, candy, powder, elixir, or concentratedsyrup formulated to dissolve in vivo, e.g., in the mouth, stomach,intestine, or colon of the subject upon oral administration.

The dosage forms described herein can be manufactured using processesthat are known to those of skill in the art. For example, for themanufacture of tablets, an effective amount of a glycan therapeuticpreparation can be dispersed uniformly in one or more excipients oradditives, for example, using high shear granulation, low sheargranulation, fluid bed granulation, or by blending for directcompression. Excipients and additives include diluents, binders,disintegrants, dispersants, lubricants, glidants, stabilizers,surfactants, antiadherents, sorbents, sweeteners, and colorants, or acombination thereof. Diluents or fillers can be used to increase thebulk of a tablet so that a practical size is provided for compression.Non-limiting examples of diluents include lactose, cellulose,microcrystalline cellulose, mannitol, dry starch, hydrolyzed starches,powdered sugar, talc, sodium chloride, silicon dioxide, titanium oxide,dicalcium phosphate dihydrate, calcium sulfate, calcium carbonate,alumina and kaolin. Binders can impart cohesive qualities to a tabletformulation and can be used to help a tablet remain intact aftercompression. Non-limiting examples of suitable binders include starch(including corn starch and pregelatinized starch), gelatin, sugars(e.g., glucose, dextrose, sucrose, lactose and sorbitol), celluloses,polyethylene glycol, alginic acid, dextrin, casein, methyl cellulose,waxes, natural and synthetic gums, e.g., acacia, tragacanth, sodiumalginate, gum arabic, xantan gum, and synthetic polymers such aspolymethacrylates, polyvinyl alcohols, hydroxypropylcellulose, andpolyvinylpyrrolidone. Lubricants can also facilitate tablet manufacture;non-limiting examples thereof include magnesium stearate, calciumstearate, stearic acid, glyceryl behenate, and polyethylene glycol.Disintegrants can facilitate tablet disintegration after administration,and non-limiting examples thereof include starches, alginic acid,crosslinked polymers such as, e.g., crosslinked polyvinylpyrrolidone,croscarmellose sodium, potassium or sodium starch glycolate, clays,celluloses (e.g., carboxymethylcelluloses (e.g., carboxymethylcellulose(CMC), CMC-Na, CMC-Ca)), starches, gums and the like. Non-limitingexamples of suitable glidants include silicon dioxide, talc, and thelike. Stabilizers can inhibit or retard drug decomposition reactions,including oxidative reactions. Surfactants can also include and can beanionic, cationic, amphoteric or nonionic. Exemplary sweeteners mayinclude stevia extract, aspartame, sucrose, alitame, saccharin, and thelike. If desired, the tablets can also comprise nontoxic auxiliarysubstances such as pH buffering agents, preservatives, e.g.,antioxidants, wetting or emulsifying agents, solubilizing agents,coating agents, flavoring agents (e.g., mint, cherry, anise, peach,apricot, licorice, raspberry, vanilla), and the like. Additionalexcipients and additives may include aluminum acetate, benzyl alcohol,butyl paraben, butylated hydroxy toluene, calcium disodium EDTA, calciumhydrogen phosphate dihydrate, dibasic calcium phosphate, tribasiccalcium phosphate, candelilla wax, carnuba wax, castor oil hydrogenated,cetylpyridine chloride, citric acid, colloidal silicone dioxide,copolyvidone, corn starch, cysteine HCl, dimethicone, disodium hydrogenphosphate, erythrosine sodium, ethyl cellulose, gelatin, glycerin,glyceryl monooleate, glyceryl monostearate, glycine, HPMC pthalate,hydroxypropylcellulose, hydroxyl propyl methyl cellulose, hypromellose,iron oxide red or ferric oxide, iron oxide yellow, iron oxide or ferricoxide, magnesium carbonate, magnesium oxide, magnesium stearate,methionine, methacrylic acid copolymer, methyl paraben, silicifiedmicrocrystalline cellulose, mineral oil, phosphoric acid, plain calciumphosphate, anhydrous calcium phosphate, polaxamer 407, polaxamer 188,plain polaxamer, polyethylene oxide, polyoxy140 stearate, polysorbate80, potassium bicarbonate, potassium sorbate, potato starch, povidone,propylene glycol, propylene paraben, propyl paraben, retinyl palmitate,saccharin sodium, selenium, silica, silica gel, fumed silica, sodiumbenzoate, sodium carbonate, sodium citrate dihydrate, sodiumcrossmellose, sodium lauryl sulfate, sodium metabisulfite, sodiumpropionate, sodium starch, sodium starch glycolate, sodium stearylfumarate, sorbic acid, sorbitol, sorbitan monooleate, pregelatinizedstarch, succinic acid, triacetin, triethyl citrate, vegetable stearin,vitamin A, vitamin E, vitamin C, or a combination thereof. The amountsof these excipients and additives can be properly selected based ontheir relation to other components and properties of the preparation andproduction method.

Immediate-release formulations of an effective amount of a glycantherapeutic composition can comprise one or more combinations ofexcipients that allow for a rapid release of a pharmaceutically activeagent (such as from 1 minute to 1 hour after administration).Controlled-release formulations (also referred to as sustained release(SR), extended-release (ER, XR, or XL), time-release or timed-release,controlled-release (CR), or continuous-release) refer to the release ofa glycan therapeutic composition from a dosage form at a particulardesired point in time after the dosage form is administered to asubject.

In one embodiment a controlled release dosage form begins its releaseand continues that release over an extended period of time. Release canoccur beginning almost immediately or can be sustained. Release can beconstant, can increase or decrease over time, can be pulsed, can becontinuous or intermittent, and the like. In one embodiment, acontrolled release dosage refers to the release of an agent from acomposition or dosage form in which the agent is released according to adesired profile over an extended period of time. In one aspect,controlled-release refers to delayed release of an agent from acomposition or dosage form in which the agent is released according to adesired profile in which the release occurs after a period of time.

In some embodiments, the dosage form can be an effervescent dosage form.Effervescent means that the dosage form, when mixed with liquid,including water and saliva, evolves a gas. Some effervescent agents (oreffervescent couple) evolve gas by means of a chemical reaction whichtakes place upon exposure of the effervescent disintegration agent towater or to saliva in the mouth. This reaction can be the result of thereaction of a soluble acid source and an alkali monocarbonate orcarbonate source. The reaction of these two general compounds producescarbon dioxide gas upon contact with water or saliva. An effervescentcouple (or the individual acid and base separately) can be coated with asolvent protective or enteric coating to prevent premature reaction.Such a couple can also be mixed with previously lyophilized particles(such as a glycan therapeutic). The acid sources can be any which aresafe for human consumption and can generally include food acids, acidand hydrite antacids such as, for example: citric, tartaric, amalic,fumeric, adipic, and succinics. Carbonate sources include dry solidcarbonate and bicarbonate salt such as sodium bicarbonate, sodiumcarbonate, potassium bicarbonate and potassium carbonate, magnesiumcarbonate and the like. Reactants which evolve oxygen or other gassesand which are safe for human consumption are also included. In oneembodiment citric acid and sodium bicarbonate are used.

In another embodiment, the dosage form can be in a candy form (e.g.,matrix), such as a lollipop or lozenge. In one embodiment an effectiveamount of a glycan therapeutic is dispersed within a candy matrix. Inone embodiment the candy matrix comprises one or more sugars (such asdextrose or sucrose). In another embodiment the candy matrix is asugar-free matrix. The choice of a particular candy matrix is subject towide variation. Conventional sweeteners (e.g., sucrose), sugar alcoholssuitable for use with diabetic patients (e.g., sorbitol or mannitol), orother sweeteners (e.g., sweeteners described herein) may be employed.The candy base can be very soft and fast dissolving, or can be hard andslower dissolving. Various forms will have advantages in differentsituations.

A candy mass composition comprising an effective amount of the glycantherapeutic can be orally administered to a subject in need thereof sothat an effective amount of the glycan therapeutic will be released intothe subject's mouth as the candy mass dissolves and is swallowed. Asubject in need thereof includes a human adult or child.

The dosage forms described herein can also take the form ofpharmaceutical particles manufactured by a variety of methods, includinghigh-pressure homogenization, wet or dry ball milling, or small particleprecipitation. Other methods useful to make a suitable powderformulation are the preparation of a solution of active ingredients andexcipients, followed by precipitation, filtration, and pulverization, orfollowed by removal of the solvent by freeze-drying, followed bypulverization of the powder to the desired particle size. In oneembodiment, the pharmaceutical particles have a final size of 3-1000microns, such as at most 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60,70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650,700, 750, 800, 850, 900, 950, 1000 microns. In another embodiment thepharmaceutical particles have a final size of 10-500 microns. In anotherembodiment the pharmaceutical particles have a final size of 50-600microns. In another embodiment the pharmaceutical particles have a finalsize of 100-800 microns.

In another embodiment, an oral dosage form is provided comprising aglycan therapeutic composition, wherein the oral dosage form is a syrup.The syrup can comprise about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, or 85% solid. The syrup cancomprise about 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% liquid, forexample, water. The solid can comprise a glycan therapeutic composition.The solid can be, for example, about 1-96%, 10-96%, 20-96%, 30-96%,40-96%, 50-96%, 60-96%, 70-96%, 80-96%, or 90-96% glycan therapeuticcomposition. In another embodiment, a glycan therapeutic composition isformulated as a viscous fluid.

In one embodiment, the composition comprises a foaming component, aneutralizing component, or a water-insoluble dietary fiber. A foamingcomponent can be at least one member selected from the group consistingof sodium hydrogencarbonate, sodium carbonate, and calcium carbonate. Inone embodiment a neutralizing component can be at least one memberselected from the group consisting of citric acid, L-tartaric acid,fumaric acid, L-ascorbic acid, DL-malic acid, acetic acid, lactic acid,and anhydrous citric acid. In one embodiment a water-insoluble dietaryfiber can be at least one member selected from the group consisting ofcrystalline cellulose, wheat bran, oat bran, cone fiber, soy fiber, andbeet fiber. The formulation can contain a sucrose fatty acid ester,powder sugar, fruit juice powder, and/or flavoring material.

In some embodiments, the dosage forms are formulated to release thepharmaceutical compositions comprising glycan therapeutic preparationsin a specific region(s) of the GI tract, such as the small or the largeintestine. In some embodiments, the dosage forms are formulated torelease the pharmaceutical compositions comprising therapeutic glycanpreparations in a specific region(s) of the GI tract, such as the cecum,ascending colon, transverse colon, descending colon, sigmoid colon,and/or rectum.

Solid formulations for oral use may comprise an enteric coating, whichmay control the location at which a glycan therapeutic composition isabsorbed in the digestive system. For example, an enteric coating can bedesigned such that a glycan therapeutic composition does not dissolve inthe stomach but rather travels to the small or the large intestine,cecum, ascending colon, transverse colon, descending colon, sigmoidcolon, and/or rectum, where it dissolves. An enteric coating can bestable at low pH (such as in the stomach) and can dissolve at higher pH(for example, in the small or large intestine or colon). Material thatcan be used in enteric coatings includes, for example, alginic acid,cellulose acetate phthalate, plastics, waxes, shellac, and fatty acids(e.g., stearic acid, palmitic acid).

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is an enzyme-responsivedelivery system. For example, trypsin responsive polymers can be madeusing hydrogels that are crosslinked by peptides that are degraded bytrypsin. Trypsin is active in the small intestine. Trypsin-responsivedelivery systems can be used to target delivery of the pharmaceuticalglycan therapeutic compositions to the small intestine. In anotherexample, enzyme-digestible hydrogels consisting of poly(vinylpyrrolidone) crosslinked with albumin are degraded in the presence ofpepsin.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is a delivery device thatenables prolonged retention at a specific site in the GI tract. Forexample, a gastroretentive delivery system enables prolonged release ofthe pharmaceutical glycan therapeutic compositions to the stomach.Gastroretentive delivery may be used for the pharmaceutical glycantherapeutic compositions that modulate bacteria in the stomach or in theupper small intestine.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is a mucoadhesive deliverysystem that adheres to the mucosal surfaces of the stomach. They aretypically composed of polymers with numerous hydrogen-bonding groups,e.g., cross-linked polyacrylic acids, sodium carboxymethyl cellulose,sodium alginate, carrageenan, Carbopol 934P, or thiolated polycarbophil.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is an expanding deliverysystem that rapidly increases in size in the stomach, which slows itspassage through the pylorus. Such systems include systems that unfold inthe stomach. For example, geometric shapes such as tetrahedrons, rings,disks, etc. can be packed into a gelatin capsule. When the capsuledissolves, the shape unfolds. The systems can be composed of one or moreerodible polymer (e.g., hydroxypropyl cellulose), one or morenonerodible polymer (e.g., polyolefins, polyamides, polyurethanes). Theglycan therapeutic may then be dispersed within the polymer matrix. Theretention times can be fine-tuned by the polymer blend. Alternatively,devices made out of elastic polymers that are stable in the acidic pH ofthe stomach but dissolve in the neutral/alkaline conditions furtheralong the GI tract can be used. Such polymer formulations can preventintestinal obstruction when the device exits the stomach. Supramolecularpolymer gels crosslinked by hydrogen bonds between carboxyl groups mayalso be used, e.g. composed of poly(acryloyl 6-aminocaproic acid)(PA6ACA) and poly(methacrylic acid-co-ethyl acrylate) (EUDRAGIT L100-55). Other systems include swellable excipients, such as collagensponges. For example, a hydrogel matrix (e.g. a swellable core:polyvinyl pyrrolidone XL, Carbopol 934P, calcium carbonate) swells 2-50times in the stomach. Superporous hydrogel composites swell to hundredsof times their original volume in a few minutes. Some systems exploitgas generation to achieve expansion, e.g. carbon dioxide-generating,expandable systems that are surrounded by a hydrophilic membrane.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is a density-controlleddelivery system. These systems are designed to either float or sink ingastric fluids which delays their emptying from the stomach. Forexample, high-density systems enable the device to settle to the bottomof the stomach, below the pylorus, and thus avoid stomach emptying.Other systems are low-density/floating systems. Such devices may, e.g.,comprise entrapped air in hollow chambers or may incorporate low-densitymaterials like fats, oils, or foam powder. Low density may be achievedthrough swelling, e.g. hydrocolloid containing capsules dissolve uponcontacting gastric fluid and the hydrocolloids swell to form a mucousbody. Alternative polymers include: chitosans, sodium alginate, andglycerol monooleate matrix. Low density may be achieved through gasgeneration. For example, tablets loaded with carbonate and optionallycitric acid generate carbon dioxide after contact with acidic aqueousmedia. The carbon dioxide generated is entrapped within the gellinghydrocolloid causing the system to float. Hydrocolloids includehydroxypropyl methylcellulose and Carbopol 934P.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein employs a design to retain adevice in the small or large intestine. The location-specific nature ofthe device is provided by a specific triggering method, e.g. pH, enzyme,etc. These include systems designed for mucoadhesion and alsomicroneedle pills. Microneedle pills comprise a drug reservoir spikedwith microneedles that is encapsulated in a pH-responsive coating. Whenthe pill reaches the desired location in the GI tract and the coatingdissolves, the microneedles enable the pill to become stuck to thelining of the GI tract. In other embodiments, the microneedle pillscomprise a capsule that consists of two chemical compartments filledwith citric acid and sodium bicarbonate, respectively. As the pilldissolves in the digestive system, barriers between the two substanceserode, allowing them to mix and create a chemical reaction that pushesmicro-needles of saccharides through the outer layer of the capsule andinto the lining of the small intestine. The saccharide needles can befilled with drugs that are delivered into nearby blood vessels as thesaccharide is absorbed.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein employs a pH sensitive polymercoating. For example, pH-dependent polymers (bi- or tri-phasic) can beinsoluble at low pH levels (e.g. acid resistance in the stomach, pH 1-2)and become increasingly soluble as pH rises, e.g. to about 5.5-6.2 inthe duodenum, to about pH 5.7 in the ascending colon, to about pH 6.4 inthe cecum, to about pH 6.6 in the transverse colon, to about pH 7.0 inthe descending colon, to about 7.2-7.5 in the ileum, or to about pH 7.5in the distal small intestine. In one example, TARGIT™ technology may beused for site-specific delivery of the pharmaceutical glycan therapeuticcompositions in the gastrointestinal (GI) tract. The system employspH-sensitive coatings onto injection-moulded starch capsules to targetthe terminal ileum and colon.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is a delayed release system ortime controlled release system. Such systems usually employ entericcoatings that may be combined with pH sensitive and time releasefunctions. For example, ETP (enteric coated time-release press coated)tablets may be used that are composed of three components: a glycantherapeutic-containing core tablet (rapid release function), apress-coated, swellable hydrophobic polymer layer (e.g. hydroxypropylcellulose layer (HPC), and a time release function. The duration of lagphase can be controlled either by weight or composition of polymer layerand an enteric coating layer (acid resistance function). In someembodiments, the dosage form for the pharmaceutical glycan therapeuticcompositions described herein employs Eudragit® enteric coatings oftablets and capsules. Other suitable synthetic polymers include:Shellac, ethyl cellulose, cellulose acetate phthalate,hydroxypropylmethyl cellulose, polyvinyl acetate phthalate and polyglutamic acid coatings, such as poly-γ-glutamic acid (γ-PGA). Thesecoatings combine both mucoadhesive and pH-dependent release strategies.To enhance colon targeted delivery Eudragits® are methacrylicco-polymers with varying side group compositions that alter the pH atwhich they are soluble. For example, for Eudragit®-coated systems nosignificant drug release occurs in the stomach (e.g. at pH 1.4) and inthe small intestine (e.g. at pH 6.3), while significant drug release canbe seen at pH 7.8 in the ileocaecal region.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is a microbial-triggeredsystem, such as a polysaccharide based delivery system. Polysaccharidebased delivery systems contain biodegradable and mucoadhesive polymercoatings, including coatings of chitosan and pectin. Other suitablenatural polymers include, e.g., guar gum, inulin, cyclodextrin, dextran,amylase, chondrotin sulphate, and locust bean gum. These deliverysystems can be used to target the glycan therapeutic to the small or thelarge intestine, cecum, ascending colon, transverse colon, descendingcolon, sigmoid colon. Coatings with naturally occurring polysaccharideslike guar gum, xanthan gum, chitosan, alginates, etc. are degraded byresident gut microbes, e.g. microbes comprising enzymes such as,xylosidase, arabinosidase, galactosidase, glucosidases, etc. In someembodiments, the microbes and associated enzyme activities arepredominatly located in a specific region of the GI tract (e.g., Jain A.et al., Perspectives of Biodegradable Natural Polysaccharides forSite-Specific Drug Delivery to the Colon, J Pharm Pharmaceut Sci10(1):86-128, 2007). For example, CODES™ technology may be used todeliver the pharmaceutical glycan therapeutic compositions. This systemcombines the polysaccharide coating with a pH-sensitive coating. In someembodiments, the system consists of a core tablet coated with threelayers of polymer coatings: The outer coating is composed of Eudragit L.This coating gets dissolved in the duodenum and exposes the nextcoating. The next coating is composed of Eudragit E. This layer allowsthe release of lactulose present in the inner core. The lactulose getsmetabolized into short chain fatty acids that lower the surrounding pHwhere the Eudragit E layer dissolves. The dissolving of Eudragit Eresults in the exposure of the glycan therapeutic. The bacteria presentin the colon are responsible for the degradation of polysaccharides thatare released from the core tablet. The degradation of polysaccharidesmay result in organic acids formation that lowers the pH of the contentssurrounding the tablet.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is a pressure-controlleddelivery system. The system employs the fact that higher pressures areencountered in the colon than in the small intestine. For example, forethylcellulose systems that are insoluble in water, the release ofglycan therapeutics occurs following disintegration of a water-insolublepolymer capsule as a result of pressure in the lumen of the colon. Therelease profile may be adjusted by varying the thickness of theethylcellulose, the capsule size and/or density of the capsule.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is a pulsatile colon targeteddelivery system. For example, the system can be a pulsincap system. Thecapsule which is employed comprises a plug that is placed in the capsulethat controls the release of the glycan therapeutic. A swellablehydrogel (e.g. hydroxyl propyl methyl cellulose (HPMC), poly methylmethacrylate or polyvinyl acetate) seals the drug content. When thecapsule gets in contact with a fluid the plug is pushed off from thecapsule and the glycan therapeutic is released. The release profile canbe controlled by varying the length and/or point of intersection of theplug with the capsule body. Another system is a port system. The capsulebody is enclosed in a semi-permeable membrane. The insoluble plugconsists of an osmotically active agent and the glycan therapeutic. Whenthe capsule gets in contact with a fluid the semi-permeable membranepermits inflow of the fluid which increases pressure in the capsulebody. This leads to an expelling of the plug and release of the glycantherapeutic.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is an osmotically controlledcolon targeted delivery system. An exemplary system, OROS-CT, consistsof osmotic units (up to 5 or 6 push pull units) encapsulated in a hardgelatin capsule. The push pull units are bilayered with outer entericimpermeable membrane and inner semi-permeable membrane. The internal,central part of the push pull consists of the drug layer and push layer.The glycan therapeutic is released through the semi-permeable membrane.The capsule body enclosing the push pull units is dissolved immediatelyafter administration. In the GI tract the enteric impermeable membraneprevents water absorption. The enteric coating is dissolved in smallintestine (higher pH, >7), water enters the unit through thesemi-permeable membrane causing push layer to swell and force out theglycan therapeutic.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is “smart pill” which can beused to release the glycan therapeutic just before reaching theileocecal valve.

In some embodiments, the dosage form for the pharmaceutical glycantherapeutic compositions described herein is a rectally administeredformulation. For example, enemas introduce a pharmaceutical glycantherapeutic composition in liquid formulation into the rectum. Thevolume administered is typically less than 10 mL. Suppositoriesintroduce a pharmaceutical glycan therapeutic composition into therectum. Suppositories are solid dosage forms that melt or dissolve wheninserted into the rectum, releasing the glycan therapeutics. Typicalexcipients for suppository formulations include cocoa butter,polyethylene glycols, and agar.

Further provided herein are methods of making a unit-dosage formdescribed herein, comprising providing a glycan therapeutic; formulatingthe glycan therapeutic into a unit-dosage form, packaging theunit-dosage form, labelling the packaged unit-dosage form, and/orselling or offering for sale the packaged and labeled unit-dosage form.

The unit-dosage forms described herein may also be processed. In oneembodiment, the processing comprises one or more of: processing thedosage form into a pharmaceutical composition, e.g., formulating,combining with a second component, e.g., an excipient or buffer or asecond active compound or therapeutic agent; portioning into smaller orlarger aliquots; disposing into a container, e.g., a gas or liquid tightcontainer; packaging; associating with a label; shipping or moving to adifferent location. In one embodiment, the processing comprises one ormore of: classifying, selecting, accepting or discarding, releasing orwithholding, processing into a pharmaceutical composition, shipping,moving to a different location, formulating, labeling, packaging,releasing into commerce, or selling or offering for sale, depending onwhether the predetermined threshold is met. In some embodiments, theprocessed dosage forms comprise a glycan therapeutic described herein.

Medical Foods

Any glycan therapeutic preparation described herein may be formulated asa medical food. A medical food is defined in section 5(b)(3) of theOrphan Drug Act (21 U.S.C. 360ee(b)(3)). Medical food is formulated tobe consumed (oral intake) or administered enterally (e.g.feeding/nasogastric tube) under medical supervision, e.g. by aphysician. It is intended for the specific dietary management of adisease or condition, such as, e.g. cancer. Medical foods as used hereindo not include food that is merely recommended by a physician as part ofan overall diet to manage the symptoms or reduce the risk of a diseaseor condition. Medical foods comprising a preparation of glycantherapeutics are administered to a subject who has a cancer or tumorunder medical supervision (which may be active and ongoing) and usually,the subject receives instructions on the use of the medical food.Medical foods may comprise, in addition to a glycan therapeuticdescribed herein, one or more food additives, color additives, GRASexcipients and other agents or substances suitable for medical foods.Medical food preparations may be nutritionally complete or incompleteformulas.

Dietary Supplements

Any glycan therapeutic preparation described herein may be formulated asa dietary supplement. Dietary supplements are regulated under theDietary Supplement Health and Education Act (DSHEA) of 1994. A dietarysupplement is a product taken by mouth that contains a “dietaryingredient” intended to supplement the diet. The “dietary ingredients”in these products may include, in addition to a glycan therapeuticdescribed herein, one or more of: vitamins, minerals, herbs or otherbotanicals, amino acids, and substances such as enzymes, organ tissues,glandulars, and metabolites. Dietary supplements can also be extracts orconcentrates, and may be found in many forms such as tablets, capsules,softgels, gelcaps, liquids, or powders. They can also be in other forms,such as a bar, but if they are, information on their label must notrepresent the product as a conventional food or a sole item of a meal ordiet. DSHEA requires that every supplement be labeled a dietarysupplement and not as a general food.

Kits

Kits are also contemplated. For example, a kit can comprise unit dosageforms of the pharmaceutical glycan therapeutic composition, and apackage insert containing instructions for use of the glycan therapeuticin treatment of a disease, disorder or pathological condition, such as,e.g., cancer. The kits include a pharmaceutical glycan therapeuticcomposition in suitable packaging for use by a subject in need thereof.Any of the compositions described herein can be packaged in the form ofa kit. A kit can contain an amount of a pharmaceutical glycantherapeutic composition (optionally additionally comprising a prebioticsubstance, a probiotic bacterium, a micronutrient, and/or a secondtherapeutic agent, such as a drug) sufficient for an entire course oftreatment, or for a portion of a course of treatment. Doses of apharmaceutical glycan therapeutic composition can be individuallypackaged, or the pharmaceutical glycan therapeutic composition can beprovided in bulk, or combinations thereof. Thus, in one embodiment, akit provides, in suitable packaging, individual doses of a glycantherapeutic composition that correspond to dosing points in a treatmentregimen, wherein the doses are packaged in one or more packets.

In one embodiment, the pharmaceutical glycan therapeutic composition canbe provided in bulk in a single container, or in two, three, four, five,or more than five containers. For example, each container may containenough of a pharmaceutical glycan therapeutic composition for aparticular week of a treatment program that runs for a month. If morethan one bulk container is provided, the bulk containers can be suitablypackaged together to provide sufficient pharmaceutical glycantherapeutic composition for all or a portion of a treatment period. Thecontainer or containers can be labeled with a label indicatinginformation useful to the subject in need thereof or the physicianperforming the treatment protocol, such as, e.g. dosing schedules.

The pharmaceutical glycan therapeutic composition can be packaged withother suitable substances, e.g., a second active compound or therapeuticagent or a buffer/carrier. The other substance or substances can bepackaged separately from the pharmaceutical glycan therapeuticcomposition, or mixed with the pharmaceutical glycan therapeuticcomposition, or combinations thereof. Thus, in one embodiment, kitsinclude a dosage form containing all the ingredients intended to be usedin a course of treatment or a portion of a course of treatment, e.g., apharmaceutical glycan therapeutic composition and optionally a secondactive compound or therapeutic agent or a buffer/carrier. In oneembodiment, a pharmaceutical glycan therapeutic composition is packagedin one package or set of packages, and additional components, such asprobiotic bacteria, prebiotics, and therapeutic agents (e.g., drugs,such as anti-cancer drugs) are packaged separately from thepharmaceutical glycan therapeutic composition.

Provided herein are kits for treating cancer in a patient comprising apackage comprising (a) a pharmaceutical composition or medical food ordietary supplement comprising a glycan therapeutic preparation describedherein, and (b) instructions for using the pharmaceutical compositionfor treating cancer (e.g., a cancer described herein) in a patient. Insome embodiments, the kit also includes a second agent which is apharmaceutical composition, e.g., a chemotherapeutic drug or otheranti-cancer drug described herein. In other examples, the kit alsocontains a probiotic.

Kits can further include written materials, such as instructions,expected results, testimonials, explanations, warnings, clinical data,information for health professionals, and the like. In one embodiment,the kits contain a label or other information indicating that the kit isonly for use under the direction of a health professional. The containercan further include scoops, syringes, bottles, cups, applicators orother measuring or serving devices.

Administration to a Subject

The glycan therapeutic preparations, pharmaceutical compositions andtherapeutic agents described herein can be administered to a subject inneed thereof by various routes (e.g., systemically or locally)including, for example, orally or parenterally, such as intravenously,intramuscularly, subcutaneously, intraorbitally, intracapsularly,intraperitoneally, intrarectally, intracisternally, intratumorally,intravasally, intradermally or by passive or facilitated absorptionthrough the skin. The therapeutic agents can be administered locally tothe site of a pathologic condition, for example, intravenously orintra-arterially into a blood vessel supplying a tumor. In someembodiments, the glycan therapeutic composition is administeredenterically. This preferentially includes oral administration, or by anoral or nasal tube (including nasogastric, nasojejunal, oral gastric, ororal jejunal). In other embodiments, administration includes rectaladministration (including enema, suppository, or colonoscopy).

Active compounds and pharmaceutical agents, e.g., prebiotic substances,probiotic bacteria or drugs, may be administered separately, e.g., priorto, concurrent with or after administration of the glycan therapeuticsand not as a part of the pharmaceutical composition or medical food ordietary supplement (e.g. as a co-formulation) of glycan therapeutics. Insome embodiments, pharmaceutical compositions or medical foodscomprising preparations of glycan therapeutics are administered incombination with a recommended or prescribed diet, e.g. a diet that isrich in probiotic and/or prebiotic-containing foods, such as it may bedetermined by a physician or other healthcare professional. Suitablesources of soluble and insoluble fibers are commercially available.Prebiotics can be found in certain foods, e.g. chicory root, Jerusalemartichoke, Dandelion greens, garlic, leek, onion, asparagus, wheat bran,wheat flour, banana, milk, yogurt, sorghum, burdock, broccoli, Brusselssprouts, cabbage, cauliflower, collard greens, kale, radish andrutabaga, and miso.

In some embodiments, the composition and metabolic activity of theintestinal bacterial community may be modified. Modification of thecomposition and metabolic activity of the intestinal bacterial communitymay be performed through the administration of i) a glycan therapeuticalone (such as in the absence of exogenously administered bacteria), ii)a glycan therapeutic and one or more beneficial microorganisms(probiotics), or iii) a combination of a glycan therapeutic, aprobiotics, and another agent, such as, e.g. a prebiotic (e.g. a dietaryfiber), or a therapeutic agent, such as, e.g. an antibacterial agent(e.g. antibiotic), an anti-inflammatory agent, an anti-cancer agent, andthe like.

In some embodiments, glycan therapeutics (e.g. oligosaccharides) have adesired degree of digestibility.

Digestibility depends on many factors, including, e.g. the degree ofpolymerization, the degree of branching, the type of glycosidiclinkages, position of the linkages, anomeric configuration (e.g. L- orD-configuration, alpha/beta configuration) of the glycan unit. Forexample, furanosides are generally more susceptible to hydrolysis thanpyranosides. Deoxy sugars are generally more acid labile than non-deoxysugars. Uronic acids are generally less susceptible to hydrolysis thannon-uronic monosaccharides.

Digestibility is a parameter that can be ascertained for the glycantherapeutics described herein. In some embodiments, glycan therapeuticsdisclosed herein are screened to assess their digestibility.Digestibility of glycan therapeutics can be assessed by any suitablemethod known in the art (e.g. by simulated gastric digestion half-life).In some embodiments, digestibility is assessed by a physiologicallyrelevant in vitro digestion reaction, e.g. simulated gastric digestionand simulated intestinal digestion. To test glycan therapeutic'sdigestibility, they can be sequentially exposed to a simulated gastricfluid (SGF) for a desired period (e.g. the length of time it takes 90%of a meal to pass from the stomach to the small intestine) and thentransferred to various GI-microbial cultures or samples. Samples atdifferent stages of the digestion (e.g., 2, 5, 15, 30, 60 and 120 min)can be analyzed by standard glycan techniques known in the art anddescribed herein. By monitoring the amount of intact glycan therapeuticsobserved over time, the half-life of digestion can be calculated.Suitable assays can be used to assess comparative digestibility (i.e.,against a benchmark glycan such as, e.g. a prebiotic) or to assessabsolute digestibility. In some embodiments, the digestibility(expressed as half-life) is 30 minutes or less, 20 minutes or less, 15minutes or less, 10 minutes or less, 5 minutes or less, 4 minutes orless, 3 minutes or less, 2 minutes or less or 1 minute or less. In someembodiments, the digestibility (expressed as half-life) is 30 minutes ormore, 45 minutes or more, 1 hour or more, 2 hours or more, 3 hours ormore, 4 hours or more, 5 hours or more, or 10 hours or more.

In some embodiments, the glycan therapeutic is digested at a constantrate and/or at a controlled rate. In such embodiments, the rate ofdigestion of the glycan therapeutic may not be optimized for the highestpossible rate of digestion. In such embodiments the rate of absorptionof the glycan therapeutic following ingestion by a mammal may be slowerand the total time period over which absorption occurs followingingestion may be longer than for glycan therapeutic of similar glycanunit composition that are digested at a faster initial rate. In someembodiments the glycan therapeutic is completely or substantiallycompletely digested. In some embodiments the glycan therapeutic issubstantially not digested or not digested.

If so desired, the glycan therapeutic composition comprisesnon-digestible oligo- or polysaccharides. In some embodiments, theglycan therapeutic is indigestible or incompletely digestible by humandigestive systems. Glycan therapeutics are, in some embodiments,selectively digested by gut microbiota constituents that allows specificchanges, both in the composition and/or activity in the commensal gutmicrobiota. In some embodiments, provided herein are glycan therapeuticsthat are non-digestible or incompletely digestible by humans in theabsence of specific microbes in the gut. In these embodiments, onlyspecific bacteria are capable of utilizing the glycan therapeutic as acarbon source.

In some embodiments, provided herein are glycan therapeutics that arenon-digestible and stimulate the growth or activity of bacteria in thedigestive system that are beneficial to the health of the body. In someembodiments, the glycan therapeutic is resistant to gastric acidity. Insome embodiments, the glycan therapeutic is resistant to hydrolysis bymammalian enzymes. In some embodiments, the glycan therapeutic isresistant to gastrointestinal absorption. In some embodiments, theglycan therapeutic is a substrate for fermentation by the intestinalmicrobiota. In some embodiments, the glycan therapeutic is a selectivesubstrate for one or a limited number of potentially beneficial bacteriain the colon, stimulating their growth and/or metabolic activity. Insome embodiments, the glycan therapeutic is capable of altering thecomposition of intestinal microbiota to a composition richer in specificbacteria. In some embodiments, the glycan therapeutic selectivelystimulates the growth and/or selective activity of intestinal bacteriaassociated with health and well-being.

In some embodiments, the glycan therapeutic capable of selectivelystimulating the growth of beneficial bacteria including Bacteroides,Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus,Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium,Roseburia, Prevotella, Bifidobacterium, Lactobacilli, Christensenellaminuta, or a Christensenellaceae in the large intestine. In someembodiments, the glycan therapeutic is digested by the gut microbiota,resulting, e.g., in the release of hydrogen and carbon dioxide gas andshort-chain fatty acids such as butyrate, if desired. A glycantherapeutic preparation, in some embodiments, promotes the selectivegrowth of beneficial colonic bacteria, including multiple species andstrains of Bifidobacteria and Lactobacilli. Bifidobacteria carry out nonhydrogen-producing lactose fermentation reactions in addition toinhibiting hydrogen producing bacteria, such as Escherichia coli.

In some embodiments, provided herein are glycan therapeutics that affectthe composition and/or activity of the intestinal microbiota. Forexample, administration of the glycan therapeutic to a subject mayresult in an increased prebiotic index. The prebiotic index (PI) relatesto the sum of: (Bifidobacteria/total bacteria)+(Lactobacilli/totalbacteria)−(Bacteroides/total bacteria)−(Clostridia/total bacteria), (seePalframan et al, 2003, Lett Appl Microbiol 37:281-284). Administrationof a glycan therapeutic to a subject may result in an increase in:Bacteroides, Blautia, Clostridium, Fusobacterium, Eubacterium,Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia,Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli,Christensenella minuta, or a Christensenellaceae.

In some embodiments, glycan therapeutics are provided that comprise betaglycosidic linkages. In some embodiments, the beta glycosidic linkagesmake the glycans substantially non-digestible and/or unabsorbable to ahuman host in the stomach and small intestine. However, certainprobiotic and commensal microbes are able to metabolize the glycans.

In some embodiments, glycan therapeutics are provided that comprisealpha glycosidic linkages. In some embodiments, the alpha glycosidiclinkages are not hydrolyzed by human salivary amylase, but can bemetabolized by Bifidobacterium bifidum and Clostridium butyricum.

In some embodiments, the therapeutic glycan is indigestible.Digestibility may differ between different enzymes or sets of enzymes,e.g. a therapeutic glycan may be digestible for certain microbesexpressing certain enzymes, but may be indigestible to a mammal lackingthe required enzyme(s) in the absence of hosting the microbes.

In some embodiments, the glycan therapeutic is an oligosaccharide thatis optionally non-digestible by a human digestive system, contains atleast one beta-glycosidic bond and/or at least one alpha-glycosidic bondthat can be digested by a bacterium. In one embodiment the bacterium isa probiotic or an endogenous commensal bacterium such as, e.g. aLactobacilli or a Bifidobacteria.

In some embodiments, the glycan therapeutics pass through the smallintestine and into the large intestine (colon) mostly intact.

In some embodiment, the glycan therapeutic comprises less than 1%, 2%,3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 14%, 16%, 18%, 20%, 30%, 40%, 50%,60%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or less than 99% of bondsthat are hydrolyzable by a mammalian amylase enzyme. One type ofhydrolyzable bonds are recognized by a mammalian amylase enzyme. Othertypes of hydrolyzable bonds (e.g. alpha 1,4; alpha 1,6, alpha 1,2; andalpha 1,6 glycosidic linkages) are recognized by specific microbialenzymes (e.g. alpha-glucosidase, cyclomaltodextrinase, neopullunanase,glucanotransferase, trehalohydrolase, and the like). Bonds may also behydrolyzable by hydrolases (e.g. Amylases, Cellulases, Mannanases,Pectinases, Pullulanases, Xylanases and the like), oxireductases(Catalases, Glucose oxidases, and the like), transferases(Fructosyltransferases, Glucosyltransferases), lyases, isomerases(Glucose isomerases), ligases, and the like. In some embodiments,glycosidic bonds are catalyzed by an enzyme and the rate of catalysiscan be measure by any suitable means known in the art and the rate canbe compared to that of another enzyme.

In some embodiments, the glycan therapeutic exhibits a slow rate offermentability by the microbiota. In some embodiments, the glycantherapeutic has a high degree of branching to resist digestion. In someembodiments, the glycan therapeutic has a DP of 10 or more, 12 or more,14 or more, 16 or more, 18 or more, 20 or more, 25 or more, 30 or moreto slow its digestibility. In some embodiments, the branching of theglycan therapeutic protects against digestion by human enzymes. In someembodiments, the size of the glycan therapeutic lessens the fermentationspeed (digestibility speed by bacteria), e.g., in the colon. In someembodiments, the glycan therapeutic characteristics promoteindigestibility by human glycosidases and promote selective digestion bythe microbiota.

In some embodiments, provided herein are glycan therapeutics that can bedigested by the microbiota (e.g. by carbohydrate fermentation) withoutcertain side effects or with a substantial reduction of symptoms offermentation, such as increased gas formation that may cause flatulence,discomfort, and/or bloating.

In one embodiment, the glycan therapeutic composition comprises one ormore mono-, oligo-, and/or polysaccharides which are non-digestible by ahuman digestive system. In another embodiment, the glycan therapeuticcomposition consists essentially of a mono-, oligo-, and/orpolysaccharide which is non-digestible by a human digestive system.

In another embodiment, the glycan therapeutic composition comprises amixture of non-digestible oligosaccharides. In another embodiment, theglycan therapeutic composition comprises one or more digestiblesaccharides and one or more non-digestible oligosaccharides. In someembodiments, the glycan therapeutic composition comprises at least onenon-digestible saccharide and optionally contains one or more digestiblemono-saccharides, oligo- or polysaccharides. In one embodiment theglycan therapeutic composition comprises a mixture of one or morenon-digestible oligosaccharides, non-digestible polysaccharides, freemonosaccharides, non-digestible saccharides, starch, or non-starchpolysaccharides.

Exemplary natural non-digestible saccharides arefructo-oligosaccharides, galacto-oligosaccharides,gluco-oligosaccharides, arabino-oligosaccharides,mannan-oligosaccharides, xylo-oligosaccharides, fuco-oligosaccharides,arabinogalacto-oligosaccharides, glucomanno-oligosaccharides,galactomanno-oligosaccharides, sialic acid comprising oligosaccharidesand uronic acid oligosaccharides.

Natural saccharides that are not digestible by humans includetransgalactooligosaccharides, galacto-oligosaccharides, lactulose,raffinose, stachyose, lactosucrose, fructo-oligosaccharides,isomalto-oligosaccharides, xylo-oligosaccharides, paratinoseoligosaccharides, difructose anhydride III, sorbitol, maltitol,lactitol, reduced paratinose, cellulose, beta-glucose, beta-galactose,beta-fructose, verbascose, galactinol, and beta-glucan, guar gum,pectin, high sodium alginate, and lambda carrageenan. Other naturalsaccharides include inulin, fructo-oligosaccharide (FOS), lactulose,galacto-oligosaccharide (GOS), raffinose, or stachyose.

Digestible monosaccharides or oligosaccharides are carbohydrates thatcan be digested by the human digestive system, and include, e.g.,lactose, galactose, or glucose.

In one embodiment, a glycan therapeutic composition is a mixture ofnon-digestible oligosaccharides and lactose, glucose or galactose.

In another embodiment, a prebiotic composition comprises a glycantherapeutic composition wherein the glycan therapeutic compositioncomprises about 1-90%, about 1-80%, about 1-70%, about 1-60%, about1-50%, about 1-40%, about 40-90%, about 40-80%, about 40-70%, about40-60%, about 40-50%, about 50-90%, about 50-80%, about 50-70%, about50-60%, about 60-90%, about 60-80%, about 60-70%, about 70-90%, about70-80%, about 70-90%, about 70-80%, about 80-90%, about 92-100%, about93-99%, about 94-98%, about 92-96%, about 93-96%, or about 93-95% glycantherapeutic by weight with the remainder comprising digestiblesaccharides. In some embodiments, the digestible saccharides are lessthan about 10% (such as about 9, 8, 7, 6, 5, 4, 3, 2, or less than 1%).In one embodiment, a glycan therapeutic composition can comprise about1-5% digestible saccharides, such as lactose, glucose or galactose. Inone embodiment the digestible saccharides are byproducts of the glycantherapeutic synthesis process.

In one embodiment, a glycan therapeutic composition comprises about1-90%, about 1-80%, about 1-70%, about 1-60%, about 1-50%, about 1-40%,about 40-90%, about 40-80%, about 40-70%, about 40-60%, about 40-50%,about 50-90%, about 50-80%, about 50-70%, about 50-60%, about 60-90%,about 60-80%, about 60-70%, about 70-90%, about 70-80%, about 70-90%,about 70-80%, about 80-90%, about 90-96%, about 93-96%, about 93-95%,about 94-98%, about 93-99%, or about 92-100% glycan therapeutic byweight and no digestible saccharides.

In one embodiment, the glycan therapeutic composition comprises one ormore non-digestible or essentially non-digestible (by a human)prebiotics. This non-digestibility is because humans lack the enzymes tobreak down some or all of the prebiotic oligosaccharide as it travelsthrough the digestive tract. When a prebiotic reaches the smallintestine and colon, bacteria (e.g., Bifidobacteria and Lactobacilli)encoding an enzyme or enzymes capable of digesting the prebiotic canbreak down the prebiotic into simple sugars that the bacteria can use.Suitable prebiotics can include one or more of a carbohydrate,carbohydrate monomer, carbohydrate oligomer, or carbohydrate polymer. Inone embodiment, the prebiotics are non-digestible saccharides, whichinclude non-digestible monosaccharides, non-digestible oligosaccharides,or non-digestible polysaccharides. In one embodiment, the glycantherapeutic composition comprises one or more of GOS, lactulose,raffinose, stachyose, lactosucrose, FOS (e.g. oligofructose oroligofructan), inulin, isomalto-oligosaccharide, xylo-oligosaccharide,paratinose oligosaccharide, transgalactosylated oligosaccharides (e.g.transgalacto-oligosaccharides), transgalactosylate disaccharides,soybean oligosaccharides (e.g. soyoligosaccharides),gentiooligosaccharides, glucooligosaccharides, pecticoligosaccharides,palatinose polycondensates, difructose anhydride III, sorbitol,maltitol, lactitol, polyols, polydextrose, reduced paratinose,cellulose, beta-glucose, beta-galactose, beta-fructose, verbascose,galactinol, and beta-glucan, guar gum, pectin, high, sodium alginate,and lambda carrageenan, or mixtures thereof. Other prebiotics includefructo-oligosaccharides (FOS), galactooligosaccharides (GOS),Xylo-oligosaccharides (XOS), chitosan oligosaccharide (chioses),isomaltose oligosaccharides (IMOS), gum arabic, soy- andpectin-oligosaccharides, pectin, xylan, inulin, chitosan, and/orbeta-glucan. Other prebiotics include various galactans and carbohydratebased gums, such as psyllium, guar, carrageen, gellan, and konjac. Otherprebiotics include dietary fibers, such as, for example, resistantmaltodextrin, fiber dextrin, polydextrose, inulin, IMOS, the linear andbranched dextrans, pullalan, hemicellulose, and combinations thereof.Dietary fiber may consist of non-starch polysaccharides such ascellulose and many other plant components such as dextrins, inulin,lignin, chitins, pectins, beta-glucans, fructo-oligosaccharides,resistant starches, soluble corn (gluco) fiber, polydextrose, and gumssuch as guar, locust bean, xanthan or pullulan gum. Other fiber sourcesinclude oligo- or polysaccharides, selected from the group consisting ofresistant maltodextrin, polydextrose, soluble corn (gluco) fiber, fiberdextrin, pullulan, resistant starch, inulin, fructo-oligosaccharides,galacto-oligosaccharides, hemicellulose and fructose oligomer syrup orlactulose or any other prebiotic compounds (including prebioticdisaccharides such as lactulose and tagatose among others). In someembodiments, both soluble and insoluble fibers are used. For example,the weight ratio of soluble fiber to insoluble fiber may be about 1:4 toabout 4:1; or about 1:1 to about 2:1.

If desired, one can target the site of fermentation from proximal, mid,to distal colon by changing the ratio of the different compounds in thecompositions described herein. Consequently, a beneficial effect may beexerted on the intestinal microbiota ecology of the subject across thelength of the entire colon.

Additional substances can be given in conjunction with a glycantherapeutic composition. These substances can enhance the action of theincreasing doses of glycan therapeutic by, e.g., encouraging the growthof bacteria in the gut that alleviate symptoms of GI diseases,increasing adhesion of probiotic or beneficial commensal bacteria, orallowing doses of probiotic bacteria to more readily pass through thestomach without being destroyed. These substances can be given prior totreatment with glycan therapeutic, during treatment with glycantherapeutic, after treatment with glycan therapeutic, or any combinationthereof. If administered during glycan therapeutic treatment, they canbe administered with the dose of glycan therapeutic being given, orbefore or after the dose of glycan therapeutic, or any combinationthereof.

Methods of Treating

Provided herein are methods of treating a disease, disorder orpathological condition comprising administering to a subject in needthereof a glycan therapeutic preparation. Also provided herein aremethods of treating cancer with a pharmaceutical composition comprisinga glycan therapeutic preparation described herein. Further providedherein are methods of treating cancer with a medical food comprising aglycan therapeutic preparation described herein. Yet further providedherein are methods of treating cancer with a dietary supplementcomprising a glycan therapeutic preparation described herein.

Provided herein are methods of treating cancer in a human subject inneed thereof. The method includes identifying a human subject in need oftreatment for a tumor or cancer, and administering to the subject apharmaceutical composition or medical food or dietary supplementcomprising a glycan therapeutic preparation described herein.

In some embodiments, the glycan therapeutic preparation is formulated asa pharmaceutical composition. In other embodiments, the glycantherapeutic preparation is formulated as a medical food. In otherembodiments, the glycan therapeutic preparation is formulated as adietary supplement.

In some embodiments, the cancer may be any solid or liquid cancer andincludes benign or malignant, non-invasive or invasive tumors,hyperplasias, and premalignant lesions, including gastrointestinalcancer (such as non-metastatic or metastatic colorectal cancer,pancreatic cancer, gastric cancer, oesophageal cancer, hepatocellularcancer, cholangiocellular cancer, oral cancer, lip cancer); urogenitalcancer (such as hormone sensitive or hormone refractory prostate cancer,renal cell cancer, bladder cancer, penile cancer); gynecological cancer(such as ovarian cancer, cervical cancer, endometrial cancer); lungcancer (such as small-cell lung cancer and non-small-cell lung cancer);head and neck cancer (e.g. head and neck squamous cell cancer); CNScancer including malignant glioma, astrocytomas, retinoblastomas andbrain metastases; malignant mesothelioma; non-metastatic or metastaticbreast cancer (e.g. hormone refractory metastatic breast cancer); skincancer (such as malignant melanoma, basal and squamous cell skincancers, Merkel Cell Carcinoma, lymphoma of the skin, Kaposi Sarcoma);thyroid cancer; bone and soft tissue sarcoma; and haematologicneoplasias (such as multiple myeloma, acute myelogenous leukemia,chronic myelogenous leukemia, myelodysplastic syndrome, acutelymphoblastic leukemia, Hodgkin's lymphoma).

In some embodiments, the cancer is acoustic neuroma; adenocarcinoma;adrenal gland cancer; anal cancer; angiosarcoma (e.g.,lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma);appendix cancer; benign monoclonal gammopathy; biliary cancer (e.g.,cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinomaof the breast, papillary carcinoma of the breast, mammary cancer,medullary carcinoma of the breast); brain cancer (e.g., meningioma,glioblastomas, glioma (e.g., astrocytoma, oligodendroglioma),medulloblastoma); bronchus cancer; carcinoid tumor; cervical cancer(e.g., cervical adenocarcinoma); choriocarcinoma; chordoma;craniopharyngioma; colorectal cancer (e.g., colon cancer, rectal cancer,colorectal adenocarcinoma); connective tissue cancer; epithelialcarcinoma; ependymoma; endotheliosarcoma (e.g., Kaposi's sarcoma,multiple idiopathic hemorrhagic sarcoma); endometrial cancer (e.g.,uterine cancer, uterine sarcoma); esophageal cancer (e.g.,adenocarcinoma of the esophagus, Barrett's adenocarcinoma); Ewing'ssarcoma; eye cancer (e.g., intraocular melanoma, retinoblastoma);familiar hypereosinophilia; gall bladder cancer; gastric cancer (e.g.,stomach adenocarcinoma); gastrointestinal stromal tumor (GIST); germcell cancer; head and neck cancer (e.g., head and neck squamous cellcarcinoma, oral cancer (e.g., oral squamous cell carcinoma), throatcancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngealcancer, oropharyngeal cancer)); hematopoietic cancers (e.g., leukemiasuch as acute lymphocytic leukemia (ALL) (e.g., B-cell ALL, T-cell ALL),acute myelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronicmyelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), and chroniclymphocytic leukemia (CLL) (e.g., B-cell CLL, T-cell CLL)); lymphomasuch as Hodgkin lymphoma (HL) (e.g., B-cell HL, T-cell HL) andnon-Hodgkin lymphoma (NHL) (e.g., B-cell NHL such as diffuse large celllymphoma (DLCL) (e.g., diffuse large B-cell lymphoma), follicularlymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma(CLL/SLL), mantle cell lymphoma (MCL), marginal zone B-cell lymphomas(e.g., mucosa-associated lymphoid tissue (MALT) lymphomas, nodalmarginal zone B-cell lymphoma, splenic marginal zone B-cell lymphoma),primary mediastinal B-cell lymphoma, Burkitt lymphoma, lymphoplasmacyticlymphoma (i.e., Waldenström's macroglobulinemia), hairy cell leukemia(HCL), immunoblastic large cell lymphoma, precursor B-lymphoblasticlymphoma and primary central nervous system (CNS) lymphoma; and T-cellNHL such as precursor T-lymphoblastic lymphoma/leukemia, peripheralT-cell lymphoma (PTCL) (e.g., cutaneous T-cell lymphoma (CTCL) (e.g.,mycosis fungoides, Sezary syndrome), angioimmunoblastic T-cell lymphoma,extranodal natural killer T-cell lymphoma, enteropathy type T-celllymphoma, subcutaneous panniculitis-like T-cell lymphoma, and anaplasticlarge cell lymphoma); a mixture of one or more leukemia/lymphoma asdescribed above; and multiple myeloma (MM)), heavy chain disease (e.g.,alpha chain disease, gamma chain disease, mu chain disease);hemangioblastoma; hypopharynx cancer; inflammatory myofibroblastictumors; immunocytic amyloidosis; kidney cancer (e.g., nephroblastomaa.k.a. Wilms' tumor, renal cell carcinoma); liver cancer (e.g.,hepatocellular cancer (HCC), malignant hepatoma); lung cancer (e.g.,bronchogenic carcinoma, small cell lung cancer (SCLC), non-small celllung cancer (NSCLC), adenocarcinoma of the lung); leiomyosarcoma (LMS);mastocytosis (e.g., systemic mastocytosis); muscle cancer;myelodysplastic syndrome (MDS); mesothelioma; myeloproliferativedisorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis(ET), agnogenic myeloid metaplasia (AMM) a.k.a. myelofibrosis (MF),chronic idiopathic myelofibrosis, chronic myelocytic leukemia (CML),chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES));neuroblastoma; neurofibroma (e.g., neurofibromatosis (NF) type 1 or type2, schwannomatosis); neuroendocrine cancer (e.g., gastroenteropancreaticneuroendocrine tumor (GEP-NET), carcinoid tumor); osteosarcoma (e.g.,bone cancer); ovarian cancer (e.g., cystadenocarcinoma, ovarianembryonal carcinoma, ovarian adenocarcinoma); papillary adenocarcinoma;pancreatic cancer (e.g., pancreatic adenocarcinoma, intraductalpapillary mucinous neoplasm (IPMN), Islet cell tumors); penile cancer(e.g., Paget's disease of the penis and scrotum); pinealoma; primitiveneuroectodermal tumor (PNT); plasma cell neoplasia; paraneoplasticsyndromes; intraepithelial neoplasms; prostate cancer (e.g., prostateadenocarcinoma); rectal cancer; rhabdomyosarcoma; salivary gland cancer;skin cancer (e.g., squamous cell carcinoma (SCC), keratoacanthoma (KA),melanoma, basal cell carcinoma (BCC)); small bowel cancer (e.g.,appendix cancer); soft tissue sarcoma (e.g., malignant fibroushistiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor(MPNST), chondrosarcoma, fibrosarcoma, myxosarcoma); sebaceous glandcarcinoma; small intestine cancer; sweat gland carcinoma; synovioma;testicular cancer (e.g., seminoma, testicular embryonal carcinoma);thyroid cancer (e.g., papillary carcinoma of the thyroid, papillarythyroid carcinoma (PTC), medullary thyroid cancer); urethral cancer;vaginal cancer; and vulvar cancer (e.g., Paget's disease of the vulva).

In some embodiments, the subject has metastatic cancer. In otherembodiments, the subject has non-metastatic cancer. In some embodiments,the subject has a benign tumor. In some embodiments, the subject has apremalignant lesion or a pre-cancerous condition. Examples ofpremalignant lesions or pre-cancerous conditions include: actinickeratosis, Barrett's esophagus, atrophic gastritis, ductal carcinoma insitu, dyskeratosis congenital, sideropenic dysphagia, lichen planus,oral submucous fibrosis, solar elastosis, cervical dysplasia,leukoplakia, and erythroplakia.

In some embodiments, the cancer is a highly immunogenic cancer, e.g.,the cancer has (e.g., as determined by analysis of a cancer biopsy) oneor more of the following characteristics: (a) tumor infiltratinglymphocytes (TIL), e.g., 1 TIL per 1000 tumor cells; (b) mutations,e.g., 0.1 or more somatic mutations per megabase of tumor genomic DNA;(c) neoantigens, e.g., 1 or more neoantigen with one or more endogenousT cell receptor and/or one or more idiotype clone that recognizes aprocessed and presented moiety of the neoantigen; (d) tertiary lymphoidstructures; (e) high expression of inflammatory gene expression, e.g.,2-fold increased expression of cytokines above baseline expression innon-cancerous tissue; and (f) immune cells exhibiting immunosuppressivephenotype, e.g. dendritic cells lacking cytokine expression. In someembodiments, the cancer is melanoma, lung cancer, bladder cancer,colorectal cancer, esophageal cancer, cervical cancer, head and neckcancer, stomach cancer, uterine cancer, liver cancer, kidney cancer,ovarian cancer, prostate cancer, myeloma, B cell lymphoma, or glioma.Methods of assessing these characteristics of the cancer are known (see,e.g., Clin Cancer Res. 2000 May; 6(5):1875-81; Nature. 2013 Aug. 22;500(7463):415-21. doi: 10.1038/nature12477. Epub 2013 Aug. 14; Nature.2014 Nov. 27; 515(7528):577-81. doi: 10.1038/nature13988; TrendsImmunol. 2014 November; 35(11):571-80. doi: 10.1016/j.it.2014.09.006.Epub 2014 Oct. 22; Front Immunol. 2013 Dec. 11; 4:438. doi:10.3389/fimmu.2013.00438; Eur J Cancer. 2009 January; 45(2):228-47. doi:10.1016/j.ejca.2008.10.026.

In some embodiments, the cancer is a primary tumor, in some embodiments,the cancer is a metastasized tumor. In some embodiments, the cancerpatient has: had one or more tumors resected, received chemotherapy orother pharmacological treatment for the cancer, received radiationtherapy, and/or received other therapy for the cancer.

In one embodiment, the method of treating a cancer in a subject includesa) administering a pharmaceutical composition comprising a glycantherapeutic preparation to a subject who has been treated with ananti-cancer therapy, b) administering an anti-cancer therapy to asubject who has been treated with a pharmaceutical compositioncomprising a glycan therapeutic preparation; or c) administering apharmaceutical composition comprising a glycan therapeutic preparationand administering an anti-cancer therapy to a subject.

In one embodiment, the method includes administering pharmaceuticalcomposition comprising a glycan therapeutic preparation to a subject whohas been treated with an anti-cancer therapy and the treatment with theanti-cancer therapy was initiated, or completed, within 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 14, 21, 28 days of initiation, or completion, of theglycan therapeutic administration.

In one embodiment, the method includes administering an anti-cancertherapy to a subject who has been treated with a pharmaceuticalcomposition comprising a glycan therapeutic preparation and thetreatment with the glycan therapeutic preparation was initiated, orcompleted, within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 21, 28 days ofinitiation, or completion, of the administration of the anti-cancertherapy.

In one embodiment, the method includes administering a pharmaceuticalcomposition comprising a glycan therapeutic preparation andadministering an anti-cancer therapy to a subject and the glycantherapeutic preparation and the anti-cancer therapy are provided within1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60minutes, hours, days, weeks of one another. In some embodiments, thefirst and second therapeutic agents (e.g. a pharmaceutical glycantherapeutic preparation and a second active compound or pharmaceuticalagent) are administered simultaneously or sequentially, in either order.The first therapeutic agent may be administered immediately, up to 1hour, up to 2 hours, up to 3 hours, up to 4 hours, up to 5 hours, up to6 hours, up to 7 hours, up to, 8 hours, up to 9 hours, up to 10 hours,up to 11 hours, up to 12 hours, up to 13 hours, 14 hours, up to hours16, up to 17 hours, up 18 hours, up to 19 hours up to 20 hours, up to 21hours, up to 22 hours, up to 23 hours up to 24 hours or up to 1-7, 1-14,1-21 or 1-30 days before or after the second therapeutic agent.

In some embodiments, the pharmaceutical composition is administered inan amount and for a time effective to result in one of (or more, e.g., 2or more, 3 or more, 4 or more of): (a) reduced tumor size, (b) reducedrate of tumor growth, (c) increased tumor cell death (d) reduced tumorprogression, (e) reduced number of metastases, (f) reduced rate ofmetastasis, (g) decreased tumor recurrence (h) increased survival ofsubject, (i) increased cancer progression free survival of subject.

In some embodiments, the method of treatment optionally results in oneor more of: i) enhancement of the subject's immune function, ii)improvement of the subject's gut health, iii) induction of production ofepithelial enzymes, iv) induction of the synthesis of vitamins in theintestines of the subject, v) reduction in the levels of toxins in thesubject's GI tract, vi) induction of apoptosis of cancer andprecancerous cells in the subject, vii) improvement of the overallgastrointestinal and colonic health of the subject, viii) reduction inbloating, abdominal distention or gas production, and/or ix) improvementof bowel regularity.

In some embodiments, methods are provided to modulate GI fluid turnover.In some embodiments, methods are provided to balance (or rebalance) GIfluid homeostasis. In some embodiments, methods are provided to modulateelectrolyte balance. Fluid loss can lead to electrolyte loss (Na, K, Mg,Cl). The methods include administering to a subject in need to GI fluidmodulation a glycan therapeutic described herein in an amount effectiveto substantially (re-)balance the fluid turnover. For example, diarrheaand constipation are conditions associated with a fluid imbalance.Osmotic diarrhea can be caused, e.g., by laxatives and sugarintolerance. Secretory diarrhea can be caused, e.g, by malabsorptionsyndromes, drugs (e.g., quinidine, quinine, colchicine, anthraquinonecathartics, castor oil, prostaglandins), and endocrine tumors thatproduce substances that increase secretion, e.g., vipomas (vasoactiveintestinal peptide), gastrinomas (gastrin), mastocytosis (histamine),medullary carcinoma of the thyroid (calcitonin and prostaglandins), andcarcinoid tumors (histamine, serotonin, and polypeptides). Some of thesemediators (e.g., prostaglandins, serotonin, and related compounds) alsoaccelerate intestinal transit, colonic transit, or both.

In some embodiments, the pharmaceutical glycan therapeutic compositionis administered in an amount and for a time effective to result inshifted or modulated state of the subject's gastrointestinal microbiota.In one embodiment, the pharmaceutical glycan therapeutic composition isadministered in an amount and for a time effective to result in shiftedor modulated bacterial taxa (one or more, two or more, three or more,etc.). In one embodiment, the pharmaceutical glycan therapeuticcomposition is administered in an amount and for a time effective toresult in shifted or modulated microbial function (e.g., a metabolicfunction). In one embodiment, the pharmaceutical glycan therapeuticcomposition is administered in an amount and for a time effective toresult in a shift or modulation of the microbiome (genome),transcriptome, metabolome, or proteome of the microbiota.

In some embodiments, administration of the pharmaceutical glycantherapeutic compositions improves the overall health of the host and/orthe health of a specific niche, such as the GI tract, e.g. by modulating(e.g. increasing or decreasing) the growth or abundance of one or moremembers of the microbial community in the niche (such as residentcommensal bacteria and/or acquired pathogens or pathobionts).

In some embodiments, administration of the glycan therapeutics describedherein improves the overall health of the gastrointestinal tract byinfluencing members of the microbial community. The glycan therapeuticsdescribed herein, e.g., activate signaling pathways within theintestinal mucosa, inhibit pathogen binding to mucosal surfaces, and/orattenuate inflammation of the intestinal mucosa. In some embodiments,administration of the glycan therapeutics results in the treatment orprevention of an inflammatory disease, including intestinalinflammation.

In one embodiment, the treatment results in increased levels of bacteriaadherent to gastrointestinal epithelial cells. For example, thetreatment results in increased levels of Citrobacter rodentium, EHECO157:H7, Candida albicans, Clostridium bolteae 90B3Clostridium cf.saccharolyticum K10, Clostridium symbiosum WAL-14673, Clostridiumhathewayi 12489931, Ruminococcus obeum A2-162, Ruminococcus gnavusAGR2154, Butyrate-producing bacterium SSC/2, Clostridium sp. ASF356,Coprobacillus sp. D6 cont1.1, Eubacterium sp. 3_1_31,Erysipelotrichaceae bacterium 21_3, Subdoligranulum sp. 4_3_54A2FAA,Ruminococcus bromii L2-63, Firmicutes bacterium ASF500, Bacteroidesdorei 5_1_36/D4 supercont2.3, Bifidobacterium animalis subsp. lactisATCC 27673, or Bifidobacterium breve UCC2003.

In some embodiments, the glycan therapeutics described herein promotethe metabolism and growth of beneficial components of the gutmicrobiota, such as, e.g., Bacteroides, Clostridium, Fusobacterium,Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Akkermansia,Faecalibacterium, Roseburia, Prevotella, Bifidobacterium, Lactobacilli,or Christensenella. As such, the glycan therapeutics may be beneficialin the treatment of diseases associated with disturbed gut microbiota.As examples, colon and liver cancers may be associated with disturbedgut microbiota.

In one embodiment, the glycan therapeutics described herein increase thelevels of Bifidobacteria. In one embodiment, the glycan therapeuticsdescribed herein increase the levels of Bacteroides. In one embodiment,the glycan therapeutics described herein increase the levels ofAkkermansia. In one embodiment, the treatment results in an increase inthe proportion of Bifidobacteria, Bacteroides, and/or Akkermansiarelative to another bacterial species.

In some embodiments, methods to protect against pathogenic infection areprovided, comprising administering to a subject a glycan therapeuticpreparation described herein. Under certain conditions, pathogenicspecies are capable of causing disease by producing infection orincreasing cancer risk for the host. A healthy human microbiota reducesthe risk of disease upon ingestion and may comprise Bacteroides,Blautia, Clostridium, Fusobacterium, Eubacterium, Ruminococcus,Peptococcus, Peptostreptococcus, Akkermansia, Faecalibacterium,Roseburia, Prevotella, Bifidobacterium, Lactobacilli, Christensenellaminuta, or a Christensenellaceae species, Streptococcus thermophilus,Enterococcus and Bacillus species, E. coli, and yeasts such asSacharomyces boulardii. A healthy bacterial community protects the host,e.g., by providing an increased barrier to translocation of bacteriaacross the gut mucosa, by competitive exclusion of potential pathogens,and by growth inhibition of bacterial pathogens.

In another embodiment, the treatment with a glycan therapeutic describedherein results in an increase in the concentration of one or moremicrobial metabolite in the GI tract (which may be measured, e.g., inthe stool). In one embodiment, the treatment with a glycan therapeuticdescribed herein results in a change (e.g., an improvement) in gutpermeability.

The glycan therapeutics described herein when administered to a subjectin an effective amount may modulate the production of one or moremicrobial metabolites. The glycan therapeutics when administered to asubject in an effective amount may modulate the production of one ormore microbial metabolites listed in Table 2. In some embodiments,glycan therapeutics when administered to a subject in an effectiveamount may modulate (e.g. increase or decrease) one or more of thefollowing microbial metabolites: formic acid, acetic acid, propionicacid, butryic acid, isobutyric acid, valeric acid, isovaleric acid,ascorbic acid, lactic acid, tryptophan, serotonin, and/or indole. Insome embodiments, glycan therapeutics when administered to a subject inan effective amount may modulate (e.g. increase or decrease) one or moreof the following microbial metabolites: succinic acid, trimethylamine(TMA), TMAO (trimethylamine N-oxide), deoxy cholic acid, ethyphenylsulfate, acetylaldehyde, hydrogen peroxide, and/or butanedione. In someembodiments, a substantial increase or decrease in a metabolite may bedetected.

In some embodiments, glycan therapeutics described herein whenadministered to a subject in an effective amount may modulate (e.g.increase) one or more of the following microbial metabolites: formicacid, acetic acid, propionic acid, butryic acid, isobutyric acid,valeric acid, isovaleric acid, acorbic acid, tryptophan, serotonin,and/or indole. In some embodiments, glycan therapeutics described hereinwhen administered to a subject in an effective amount may modulate (e.g.decrease) one or more of the following microbial metabolites: Succinicacid, TMAO, deoxy cholic acid, ethyphenyl sulfate, acetylaldehyde,and/or butanedione. In some embodiments, glycan therapeutics describedherein when administered to a subject in an effective amount maymodulate (e.g. decrease) one or more of the following microbialmetabolites: formic acid, acetic acid, propionic acid, butryic acid,isobutyric acid, valeric acid, isovaleric acid, acorbic acid,tryptophan, serotonin, and/or indole. In some embodiments, glycantherapeutics described herein when administered to a subject in aneffective amount may modulate (e.g. increase) one or more of thefollowing microbial metabolites: Succinic acid, TMAO, deoxy cholic acid,ethyphenyl sulfate, acetylaldehyde, and/or butanedione.

In some embodiments, the glycan therapeutic is digested by the gutmicrobiota resulting, e.g., in the release of short-chain fatty acidssuch as butyrate, acetate, and propionate, which may actimmunomodulatory (e.g. anti-inflammatory) and other metabolites (e.g.bile acids, and lactate) that may confer beneficial health effects onthe host.

Some methods described herein include the administration of glycantherapeutics to modulate the host's immune functions and/or intestinalepithelial cell functions. The glycan therapeutics may upregulate theimmune function, e.g. to improve the ability of the host to fightcancers, while downregulation of immune function may treat inflammation(such as, e.g., intestinal inflammation). Modulated beneficial bacteriamay stimulate intestinal epithelial cell responses, includingrestitution of damaged epithelial barrier, production of antibacterialsubstances and cell-protective proteins, and blocking ofcytokine-induced intestinal epithelial cell apoptosis.

In some embodiments, method of modulating a functional pathway of themicrobiota of the gastrointestinal tract are provided. The methodsinclude administering to the human subject a pharmaceutical compositioncomprising a glycan therapeutic preparation in an amount effective tomodulate the functional pathway. In some embodiments, the functionalpathway modulates the production of anti-microbial agent, a secondarybile acid, a short-chain fatty acid, a siderophore or a metabolitelisted in Table 2 by the microbiota.

Bacteria can elicit both pro- and anti-inflammatory responses from host(mammalian) cells. In one embodiment, glycan therapeutics are used toalter the bacterial population or its function to elicit a desired hostresponse. The host response may be modulated a) via secreted or shedbacterial products (e.g., short-chain fatty acids), b) stimulation ofthe production of antimicrobial peptides (AMPs), c) modulation(increasing or decreasing the production of) inflammatory andimmunomodulatory cytokines including: interleukin-1α (IL-1α), IL-1β,IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-13, IL-17A, IL-17F, IL-22,IL-23, tumor necrosis factor (TNF), chemokine (C—C motif) ligand 5(CCL5, also known as RANTES), transforming growth factor beta (TGF-β),interferon gamma (IFN-γ), or d) modulation of other innate or adaptiveimmune responses.

The glycan therapeutics when administered to a subject in an effectiveamount may modulate one or more host pathways. In some embodiments, aninflammatory state, e.g. of the GI tract is modulated by administrationof a glycan therapeutic. In some embodiments, production of short-chainfatty acids (SCFAs) may be modulated. For example, SCFAs produced by thegut microbiota may serve as energy sources for colonic epithelial cellsand in some embodiments contribute to the maintenance of gut barrierfunction. In some instances, increased gut barrier function limitsplasma endotoxin levels and prevents systemic inflammation (Cani et al.,Changes in gut microbiota control inflammation in obese mice through amechanism involving GLP-2-driven improvement of gut permeability, Gut,2009, 58:1091). In some embodiments, SCFAs promote gut barrier functionby affecting mucin production and gastrointestinal peptide LL-37. SCFAsmodulate a number of human immunological factors. In some embodiments,SCFAs modulate inflammation by suppressing NF-kB and the production ofinflammatory cytokines such as IL-6 and TNF-α (Kim C H et al. 2014. GutMicrobiota-Derived Short-Chain Fatty Acids, T Cells, and Inflammation.Immune Network 14(6):277-288). In one embodiment, treatment with aglycan therapeutic described herein modulates (e.g., increases) thatSCFA propionate. In some embodiments, propionate increases expression ofFoxp3, a T cell regulatory factor, and/or IL-10, an anti-inflammatorycytokine, in colonic regulatory T cells. In some embodiments, SCFAspromote the generation of (e.g., colonic) regulatory T (Treg) cellsand/or CD4+ T cells thereby limiting inflammatory responses (Arpaia etal., Metabolites produced by commensal bacteria promote peripheralregulatory T-cell generation, Nature, 2013, 504:451; Smith P M et al.2013. The microbial metabolites, short chain fatty acids, regulatecolonic Treg cell homeostasis. Science; 341(6145)).

In some embodiments, glycan therapeutics are administered to modulateshort chain fatty acid (SCFA) production of commensal bacteria includingmembers of the families Ruminocaccaceae and Lachnospiraceae (Vital M,Howe A C, Tiedje J M. 2014. Revealing the bacterial butyrate synthesispathways by analyzing (meta)genomic data. mBio 5(2):e00889-14.doi:10.1128/mBio.00889-14). In some embodiments, glycan therapeuticswhen administered in an effective amount modulate bacterial species thatproduce SCFAs, such as, e.g., those of the Ruminocacceae family and/orLachnospiraceae family. In some embodiments, the glycan therapeuticsmodulate host immunity and inflammation.

In some embodiments, glycan therapeutics are administered to inducesystemic effects, e.g. of SCFAs and other microbially producedimmunomodulatory molecules or metabolites to modulate the inflammatorystate of distal sites.

In some embodiments, the treatment with the glycan therapeuticsdescribed herein results in increased levels of Th17 or Th1 cells in thesubject. In some embodiments, the treatment with the glycan therapeuticsdescribed herein results in increased levels of cytotoxic T-cells ornatural killer cells in the subject. In some embodiments, the treatmentwith the glycan therapeutics described herein promote the growth ofimmune cells of the subject. In some embodiments, the treatment with theglycan therapeutics described herein promotes the differentiation ofimmune cells of the subject. In some embodiments, the treatment with theglycan therapeutics described herein results in increased tumorsurveillance. In some embodiments, the treatment with the glycantherapeutics described herein results in increased anti-tumor activityof the host's immune system.

In some embodiments, the glycan therapeutics promote the growth ofbeneficial taxa (e.g., Bacteroides and Bifidobacteria). In someembodiments, promoting growth of certain taxa modulates (e.g.upregulates) the immune response of the host.

In some embodiments, the treatment with the glycan therapeuticsdescribed herein results an increase in tumor-infiltrating bacteria,e.g., in the GI tract that may infiltrate gastrointestinal tumors. Insome embodiments, the treatment with the glycan therapeutics describedherein results an increase of bacteria that produce toxins and/orsmall-molecules that decrease the growth of cancers or increase celldeath of cancer cells, e.g., that of gastrointestinal cancers. In someembodiments, the treatment with the glycan therapeutics described hereinresults in the production of microbial metabolites that are toxic to thetumor or repress oncogene expression or oncogenic metabolism.

In some embodiments, methods of selecting a subject for a treatment(e.g., for treatment with a pharmaceutical composition, medical food ordietary supplement) are provided. The methods include: (a) identifying asubject who has a tumor or cancer (e.g., a tumor or cancer describedherein), and (b) selecting the identified subject for treatment with aglycan therapeutic preparation described herein. In some embodiments,the subject is further selected for treatment with a second anti-cancerdrug or therapy (e.g., a second anti-cancer drug or therapy describedherein).

In some embodiments, methods of selecting a subject for a treatmentinclude selecting a subject that is treatment naïve. In someembodiments, the subject is treatment naïve with respect to ananti-cancer therapy, such as, e.g., chemotherapy, radiation therapy orsurgical removal of the tumor. In some embodiments, the subject istreatment naïve with respect to an immune suppressive therapy. In someembodiments, the subject is treatment naïve with respect to anantimicrobial therapy.

In some embodiments, methods of selecting a subject for a treatmentinclude selecting the glycan therapeutic preparation on the basis thatit will provide therapeutic benefit to the subject. In some embodiments,methods of selecting a subject for a treatment include selecting thesubject on the basis that the subject will or is expected to benefitfrom administration of the glycan therapeutic preparation.

In some embodiments, the selection methods include assessing thesubject's gastrointestinal microbiota, e.g., before, during and/or afterthe treatment. In one embodiment, the subject's gastrointestinalmicrobiota is assessed before starting treatment. In some embodiments,the results of the assessment are used to select the subject fortreatment. Alternatively or in addition, assessment is used to identifya dosage or dosage regimen for the treatment.

In some embodiments, subjects are identified and selected that respondto a glycan therapeutic for initial and/or continued treatment.Responders may be identified using one or more suitable parameter asdetermined by a physician or other healthcare provider. The parametersinclude one or more of: a) a physiological treatment effect (e.g.reduction of a fever, increased well-being, increased energy, etc.), b)a desired change in a (host) biomarker (e.g. a cancer marker, aninflammatory marker, etc.), c) a microbial taxa shift (e.g., in relativeabundance, change in diversity, etc.), d) a functional shift of themicrobiota (e.g. a shift in metabolic output, microbial signaling,microbial gene expression, microbial protein expression), e) absence orpresence of a desired bacterial taxa (in the host microbiota), etc. Insome embodiments, non-responders are identified and selected. In oneembodiment, treatment methods include rendering the non-responderresponsive to the treatment. In some embodiments, this may includeadministering to the non-responder one or more bacterial taxa (e.g. oneor more commensals) that are responsive to glycan (and/or second agent)treatment.

In some embodiments, methods of evaluating a subject, e.g., to evaluatesuitability for glycan treatment, responsiveness to glycan treatment, orglycan treatment progression, are provided. Optionally, the glycantreatment is in combination with another treatment or therapy (e.g., adrug treatment, such as an anti-cancer drug). Changes in a variety ofsuitable biomarkers may be assessed. In some embodiments, changes in themicrobiota are assessed or corresponding values are acquired. In someembodiments, changes in microbial metabolism (e.g. metabolite inputand/or output) are assessed or corresponding values are acquired. Insome embodiments, changes in the microbiome (e.g. changes on the genomeor transcriptome level) are assessed or corresponding values areacquired. In some embodiments, changes in the microbial proteome areassessed or corresponding values are acquired. In some embodiments,changes in the host (e.g., metabolic, inflammatory, cardio-vascular,etc.) are assessed or corresponding values are acquired. In someembodiments, changes in the host proteome (e.g. protein synthesis),metabolome, transcriptome (e.g. gene transcription/expression), cellsignaling, etc. are assessed or corresponding values are acquired. Insome embodiments, the methods include a) acquiring a value for aparameter related to the level of a biomarker modulated by a glycantherapeutic preparation (and/or the drug or therapy in a combinationtreatment); b) responsive to the value, classifying the subject,selecting a treatment for the subject, or administering the treatment tothe subject, thereby evaluating a subject.

Treatment responsiveness and/or progression may be assessed or evaluatedusing one or more biomarker. Suitable biomarkers may be determined by aphysician and may include: i) changes in gastrointestinal microbiota andthe overall metabolism of the gastric environment, such as theproduction of organic acids (e.g., SCFAs), ii) modulation of the immunesystem, assessing inflammatory and immune globulins iii) increase theabsorption of minerals in the colon, such as calcium, zinc or magnesiumiv) regulation of lipid metabolism, lowering cholesterol, v) inductionof other important processes for host homeostasis (see, reviews byPool-Zobel B L. Inulin-type fructans and reduction in colon cancer risk:review of experimental and human data. 2005. British Journal ofNutrition 93 Suppl 1:S73-90; and Liong M T. Roles of Probiotics andPrebiotics in Colon Cancer Prevention: Postulated Mechanisms and In-vivoEvidence. 2008. International Journal of Molecular Sciences9(5):854-63).

The glycan therapeutic treatment may result in increases or decreases ofone or more biomarkers that can be determined by methods known in theart. An investigator can determine at which point or points duringtreatment the biomarker(s) should be measured, e.g. prior to treatment,at various intervals during treatment and/or after treatment. Anysuitable sample, e.g. a gastrointestinal-specific sample such as, e.g. atissue sample or biopsy, a swab, a gastrointestinal secretion (such asfeces/a stool sample), etc. may be drawn from the subject and the samplemay be analyzed by suitable methods known in the art. In someembodiments, a substantial increase or decrease in a biomarker may bedetected to assess treatment progression.

In some embodiments, treatment with the glycan therapeutic results inthe release of short-chain fatty acids such as butyrate, acetate, andpropionate and other metabolites (e.g. bile acids, and lactate) by themicrobiota that may affect one or more biological pathways of the hostsubject (e.g. have an immunomodulatory effect on the host).

To evaluate the effect of administered pharmaceutical glycan therapeuticcompositions on SCFA production in the gut, fecal samples can becollected. SCFA levels, particularly acetate, propionate, and butyratemay be quantified. SCFAs, creatines, and hydroxy-SCFAs can be quantifiedby alkalinizing stool samples, obtaining fingerprints of the metaboliccomposition of the sample using, e.g., 1D 1H NMR spectrometer, andanalyzing with supervised multivariate statistical methods. Inulin mayserve as a positive control.

In some embodiments, microbial metabolite profiles of patient samples ormicrobes cultures from subject samples are used to identify risk factorsfor developing a disease, disorder or condition, such as, e.g., cancer.Exemplary metabolites for the purposes of diagnosis, prognostic riskassessment, or treatment assessment purposes include those listed inTable 2. In some embodiments, microbial metabolite profiles are taken atdifferent time points during a subject's disease and treatment in orderto evaluate the subject's disease state including recovery or relapseevents, e.g., that of a tumor. In some embodiments, metabolite profilesare acquired to inform subsequent treatment.

Provided herein are methods of treating cancer in a human subject inneed thereof with a combination therapy. The method includesadministering to the human subject a first agent which is apharmaceutical composition or medical food or dietary supplementcomprising a glycan therapeutic preparation described herein incombination with a second agent.

In some embodiments, the glycan therapeutics described herein may beused in combination with other anti-proliferative, anti-neoplastic oranti-tumor drugs or treatments. Such drugs or treatments includechemotherapeutic drugs, e.g., cytotoxic drugs (e.g., alkylating agents,antimetabolites, anti-tumor antibiotics, topoisomerase inhibitors,mitotic inhibitors, corticosteroids); cancer growth blockers such astyrosine kinase inhibitors and proteasome inhibitors; other chemicaldrugs such as L-asparaginase and bortezomib (Velcade®). Hormonetherapies (or anti-hormone therapies) may be used, e.g., forhormone-sensitive cancers.

In some embodiments, the glycan therapeutics described herein may beused in combination with other anti-proliferative, anti-neoplastic oranti-tumor drugs or treatments that include an anti-cancer drug, suchas, e.g., checkpoint inhibitors (such as, e.g., anti-PD-1, anti-PD-L1,anti-CTLA4, anti-TIM-3, anti-LAG-3); vaccines (such as, e.g., autologouscancer vaccines, allogeneic cancer vaccines, neoantigen cancer vaccines,shared antigen cancer vaccines (e.g. NY-ESO-1)); targeted kinaseinhibitors (such as, e.g., Imatinib mesylate, Ibrutinib, Neratinib,Palpociclib, Erlotinib, Lapatinib); antibodies (such as, e.g.,Bevacizumab, Trastuzumab, Rituximab, Cetuximab); chemotherapeutics (suchas, e.g., irinotecan, 5-flurouracil, lenalidomide, capecitabine,docetaxel), antibody-drug conjugates (e.g. ado-trastuzumab emtansine).

Immunotherapies are another class of anti-cancer agent that may be usedin the combination with glycan therapeutics. Immunotherapies includecheckpoint inhibitors (see, e.g., PMID: 26598056, PMID: 26680224); Tcell therapy (e.g., CAR-T cell therapy) (see, e.g., PMID: 26611350),Natural Killer (NK) cell immunomodulation (see, e.g., PMID: 26697006);and cancer vaccines (PMID: 26579225).

The glycan therapeutics described herein may be used in combination withnon-drug therapies for cancer such as surgery, radiotherapy, orcryotherapy. Treatment methods may include glycan therapeutics describedherein in combination with 2 or more other therapies or drugs. Forexample, breast cancer may be treated with a combination of glycantherapeutics described herein and surgery or radiotherapy and achemotherapeutic cocktail or biologic (e.g., an anti-HER2 antibody).

The glycan therapeutics described herein may be used in combination withone or more of: a pain-management drug an antidepressant, anantiepileptic, a steroid, a drug for managing a GI tract motilitydisorder, an anti-inflammatory agent, and an antimicrobial agent,described elsewhere herein.

In one embodiment, the second agent is a therapeutic agent which is animmune checkpoint modulator. The checkpoint modulator may be aninhibitory or agonist form of the following: antibody (e.g., amonospecific antibody such as a monoclonal antibody (mAb), e.g., ahumanized or fully human mAb); a fusion protein, e.g., an Fc-receptorfusion protein; or a small molecule. The check point modulator maymodulate a checkpoint protein or a ligand of a checkpoint protein. Inone embodiment, the checkpoint modulator is an inhibitor (e.g., aninhibitory antibody or small molecule inhibitor) of CTLA-4 (e.g., ananti-CTLA4 antibody such as ipilimumab/Yervoy or tremelimumab). In otherembodiments, the checkpoint modulator is an inhibitor (e.g., aninhibitory antibody or small molecule inhibitor) of PD-1 (e.g.,nivolumab/Opdivo®; pembrolizumab/Keytruda®; pidilizumab/CT-011). Inother embodiments, the checkpoint modulator is an inhibitor (e.g., aninhibitory antibody or small molecule inhibitor) of PDL1 (e.g.,MPDL3280A/RG7446; MEDI4736; MSB0010718C; BMS 936559). In yet otherembodiments, the checkpoint modulator is an inhibitor (e.g., aninhibitory antibody or Fc fusion or small molecule inhibitor) of PDL2(e.g., a PDL2/Ig fusion protein such as AMP 224). In other embodiments,the checkpoint modulator modulates (e.g., an antibody modulator or smallmolecule modulator) B7-H3 (e.g., MGA271), B7-H4, BTLA, HVEM, TIM3, GAL9,LAG3, VISTA, KIR, 2B4, CD160, CGEN-15049, CHK 1, CHK2, A2aR, B-7 familyligands, or a combination thereof.

In one embodiment, the second agent is a therapeutic agent which is anadoptive T cell (CAR-T cell) or NK cell for anti-cancer therapy. In oneembodiment, the adoptive T cell therapy comprises administering to asubject autologous and/or allogeneic T-cells. In another embodiment, theautologous and/or allogeneic T-cells are targeted against tumor antigens(e.g., CD19, CD20, CD22, AFP, CEA, CA-125, MUC-1, ETA, MAGE, CA15-3,CA27-29, CA19-9, CD34, CD117, PSA, MART-1 etc.). In one embodiment, theadoptive NK cell therapy comprises administering to a subject autologousand/or allogeneic NK cells.

In one embodiment, the second agent is a therapeutic agent which is acancer vaccine (e.g., a tumor cell vaccine, an antigen vaccine, adendritic cell vaccine, a DNA vaccine, or vector based vaccine). Thetherapeutic cancer vaccine may be a dendritic cell vaccine, e.g., adendritic cell vaccine composed of autologous dendritic cells and/orallogeneic dendritic cells. In certain embodiments, the autologous orallogeneic dendritic cells are loaded with cancer antigens prior toadministration to the subject. In certain embodiments, the autologous orallogeneic dendritic cells are loaded with cancer antigens throughdirect administration to the tumor. The therapeutic cancer vaccine maybe a peptide vaccine, e.g. synthetic peptides formulated to elicit ananti-cancer response from the host immune system. In certainembodiments, the peptides encode tumor antigens. In certain embodiments,the tumor antigens encoded by the peptides are neoantigens.

In one embodiment, the second agent is a therapeutic agent which is achemotherapeutic agent (e.g., a cytotoxic agent or other chemicalcompound useful in the treatment of cancer). These include alkylatingagents, antimetabolites, folic acid analogs, pyrimidine analogs, purineanalogs and related inhibitors, vinca alkaloids, epipodopyyllotoxins,antibiotics, L-asparaginase, topoisomerase inhibitors, interferons,platinum coordination complexes, anthracenedione substituted urea,methyl hydrazine derivatives, adrenocortical suppressant,adrenocorticosteroides, progestins, estrogens, antiestrogen, androgens,antiandrogen, and gonadotropin-releasing hormone analog. Also includedis 5-fluorouracil (5-FU), leucovorin (LV), irenotecan, oxaliplatin,capecitabine, paclitaxel and doxetaxel. Non-limiting examples ofchemotherapeutic agents include alkylating agents such as thiotepa andcyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan andpiposulfan; aziridines such as benzodopa, carboquone, meturedopa, anduredopa; ethylenimines and methylamelamines including altretamine,triethylenemelamine, trietylenephosphoramide,triethiylenethiophosphoramide and trimethylolomelamine; acetogenins(especially bullatacin and bullatacinone); a camptothecin (including thesynthetic analogue topotecan); bryostatin; callystatin; CC-1065(including its adozelesin, carzelesin and bizelesin syntheticanalogues); cryptophycins (particularly cryptophycin 1 and cryptophycin8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189and CB1-TM1); eleutherobin; pancratistatin; a sarcodictyin;spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine,cholophosphamide, estramustine, ifosfamide, mechlorethamine,mechlorethamine oxide hydrochloride, melphalan, novembichin,phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureassuch as carmustine, chlorozotocin, fotemustine, lomustine, nimustine,and ranimnustine; antibiotics such as the enediyne antibiotics (e.g.,calicheamicin, especially calicheamicin gammall and calicheamicinomegall (see, e.g., Agnew, Chem. Intl. Ed Engl. 33:183-186 (1994));dynemicin, including dynemicin A; bisphosphonates, such as clodronate;an esperamicin; as well as neocarzinostatin chromophore and relatedchromoprotein enediyne antiobiotic chromophores), aclacinomysins,actinomycin, authramycin, azaserine, bleomycins, cactinomycin,carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin,daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, ADRIAMYCIN®doxorubicin (including morpholino-doxorubicin,cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin anddeoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin,mitomycins such as mitomycin C, mycophenolic acid, nogalamycin,olivomycins, peplomycin, potfiromycin, puromycin, quelamycin,rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex,zinostatin, zorubicin; anti-metabolites such as methotrexate and5-fluorouracil (5-FU); folic acid analogues such as denopterin,methotrexate, pteropterin, trimetrexate; purine analogs such asfludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidineanalogs such as ancitabine, azacitidine, 6-azauridine, carmofur,cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine;androgens such as calusterone, dromostanolone propionate, epitiostanol,mepitiostane, testolactone; anti-adrenals such as aminoglutethimide,mitotane, trilostane; folic acid replenisher such as frolinic acid;aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil;amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine;diaziquone; elfomithine; elliptinium acetate; an epothilone; etoglucid;gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids suchas maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol;nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone;podophyllinic acid; 2-ethylhydrazide; procarbazine; PSK® polysaccharidecomplex (JHS Natural Products, Eugene, Oreg.); razoxane; rhizoxin;sizofuran; spirogermanium; tenuazonic acid; triaziquone;2,2′,2″-trichlorotriethylamine; trichothecenes (especially T-2 toxin,verracurin A, roridin A and anguidine); urethan; vindesine; dacarbazine;mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine;arabinoside (“Ara-C”); cyclophosphamide; thiotepa; taxoids, e.g.,Taxol®, paclitaxel (Bristol-Myers Squibb Oncology, Princeton, N.J.),ABraxane®. Cremophor-free, albumin-engineered nanoparticle formulationof paclitaxel (American Pharmaceutical Partners, Schaumberg, Ill.), andTAXOTERE® doxetaxel (Rhone-Poulenc Rorer, Antony, France); chloranbucil;GEMZAR® gemcitabine; 6-thioguanine; mercaptopurine; methotrexate;platinum coordination complexes such as cisplatin, oxaliplatin andcarboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide;mitoxantrone; vincristine; NAVELBINE® vinorelbine; novantrone;teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate;irinotecan (e.g., CPT-11); topoisomerase inhibitor RFS 2000;difluoromethylornithine (DMFO); retinoids such as retinoic acid;capecitabine; and pharmaceutically acceptable salts, acids orderivatives of any of the above. Two or more (e.g., three, four, five,etc.) chemotherapeutic agents can be used in a cocktail to beadministered in combination with the first therapeutic agent describedherein. Suitable dosing regimens of combination chemotherapies are knownin the art and described in, for example, Saltz et al. (1999) Proc ASCO18:233a and Douillard et al. (2000) Lancet 355:1041-7.

In one embodiment, the second agent is a therapeutic agent which is abiologic such a cytokine (e.g., interferon or an interleukin (e.g.,IL-2)). In other embodiments, the biologic is an immunoglobulin-basedbiologic, e.g., a monoclonal antibody (e.g., a humanized antibody, afully human antibody, an Fc fusion protein or a functional fragmentthereof) that agonizes a target to stimulate an anti-cancer response, orantagonizes an antigen promoting cancer growth or maintainance. Suchagents include Rituxan (Rituximab); Zenapax (Daclizumab); Simulect(Basiliximab); Synagis (Palivizumab); Remicade (Infliximab); Herceptin(Trastuzumab); Mylotarg (Gemtuzumab ozogamicin); Campath (Alemtuzumab);Zevalin (Ibritumomab tiuxetan); Humira (Adalimumab); Xolair(Omalizumab); Bexxar (Tositumomab-I-131); Raptiva (Efalizumab); Erbitux(Cetuximab); Avastin (Bevacizumab); Tysabri (Natalizumab); Actemra(Tocilizumab); Vectibix (Panitumumab); Lucentis (Ranibizumab); Soliris(Eculizumab); Cimzia (Certolizumab pegol); Simponi (Golimumab); Ilaris(Canakinumab); Stelara (Ustekinumab); Arzerra (Ofatumumab); Prolia(Denosumab); Numax (Motavizumab); ABThrax (Raxibacumab); Benlysta(Belimumab); Yervoy (Ipilimumab); Adcetris (Brentuximab Vedotin);Perjeta (Pertuzumab); Kadcyla (Ado-trastuzumab emtansine); and Gazyva(Obinutuzumab). Also included are antibody-drug conjugates.

In one embodiment, the second agent is an immunomodulatory drug, e.g.,ABREVA (docosanol), Acyclovir, Agenerase (amprenavir), Albenza(albendazole), Aldara (imiquimod), Alinia (nitazoxanide), Allegra-D,Altabax (retapamulin), Amevive (alefacept), Aphthasol, Aptivus(tipranavir), Aptivus (tipranavir), Arcapta (indacaterol maleateinhalation powder), Astepro (azelastine hydrochloride nasal spray),Avelox I.V. (moxifloxacin hydrochloride), AzaSite (azithromycin),Baraclude (entecavir), Benlysta (belimumab), Bepreve (bepotastinebesilate ophthalmic solution), Berinert (C1 Esterase Inhibitor (Human)),Besivance (besifloxacin ophthalmic suspension), Biaxin XL(clarithromycin extended-release tablets), Cancidas, Carrington patch,Cayston (aztreonam for inhalation solution), Cedax (ceftibuten),Cefazolin and Dextrose USP, CellCept, Cervarix [Human PapillomavirusBivalent (Types 16 and 18) Vaccine, Recombinant, Children's Motrin Cold,Cinryze (C1 Inhibitor (Human)), Clarinex, Clarithromycin (Biaxin),Clemastine fumarate syrup, Cleocin (clindamycin phosphate), Coartem(artemether/lumefantrine), Combivir, Complera(emtricitabine/rilpivirine/tenofovir disoproxil fumarate), Condylox Gel0.5% (pokofilox), Cosentyx (secukinumab), Crixivan (Indinavir sulfate),Daliresp (roflumilast), Daptacel, Descovy (emtricitabine and tenofoviralafenamide), Dificid (fidaxomicin), Doribax (doripenem), Dynabac,Edurant (rilpivirine), Egrifta (tesamorelin for injection), Entyvio(vedolizumab), Envarsus XR (tacrolimus extended-release), Epivir(lamivudine), Eraxis (anidulafungin), Evotaz (atazanavir andcobicistat), Evoxac, Extina (ketoconazole), Famvir (famciclovir), Famvir(famciclovir), Firazyr (icatibant), Flagyl ER, Flonase Nasal Spray,Flublok (seasonal influenza vaccine), Flucelvax, Influenza VirusVaccine, FluMist (Influenza Virus Vaccine), Fluzone Preservative-free,Fortovase, Fulyzaq (crofelemer), Fuzeon (enfuvirtide), Gardasil(quadrivalent human papillomavirus (types 6, 11, 16, 18) recombinantvaccine), Gastrocrom Oral Concentrate (cromolyn sodium), Genvoya(elvitegravir, cobicistat, emtricitabine, and tenofovir alafenamide),Gralise (gabapentin), Grastek (Timothy Grass Pollen Allergen Extract),Havrix, Hepsera (adefovir dipivoxil), Hiberix (Haemophilus b ConjugateVaccine; Tetanus Toxoid Conjugate), Horizant (gabapentin enacarbil),HyQvia [Immune Globulin Infusion 10% (Human) with Recombinant HumanHyaluronidase], Ilaris (canakinumab), Incivek (telaprevir), IncruseEllipta (umeclidinium inhalation powder), INFANRIX (Diphtheria andTetanus Toxoids and Acellular Pertussis Vaccine Adsorbed), INFERGEN(interferon alfacon-1), Intelence (etravirine), Intron A (Interferonalfa-2b, recombinant), Intron A (interferon alfa-2b, recombinant),Invirase (saquinavir), Isentress (raltegravir), Ixiaro (JapaneseEncephalitis Vaccine, Inactivated, Adsorbed), Kalbitor (ecallantide),Kaletra Capsules and Oral Solution, Ketek (telithromycin), Kineret,anakinra, Lamisil (terbinafine hydrochloride) Solution, 1%, Lamisil(terbinafine hydrochloride) Tablets, Leukine (sargramostim), Lexiva(fosamprenavir calcium), Lotrisone (clotrimazole/betamethasonediproprionate) lotion, Lovenox (enoxaparin sodium) Injection, Makena(hydroxyprogesterone caproate injection), Malarone (atovaquone;proguanil hydrochloride) Tablet, Menveo (meningitis vaccine), Moxatag(amoxicillin), Myalept (metreleptin for injection), Norvir (ritonavir),Noxafil (posaconazole), Nulojix (belatacept), Odefsey (emtricitabine,rilpivirine, and tenofovir alafenamide), Oral Cytovene, Oralair (SweetVernal, Orchard, Perennial Rye, Timothy and Kentucky Blue Grass MixedPollens Allergen Extract), Oravig (miconazole), Otezla (apremilast),Panretin Gel, Pediarix Vaccine, Peg-Intron (peginterferon alfa-2b),Pegasys (peginterferon alfa-2a), Plegridy (peginterferon beta-1a),Prevnar 13 (Pneumococcal 13-valent Conjugate Vaccine), Prezcobix(darunavir and cobicistat), Prezista (darunavir), Qnasl (beclomethasonedipropionate) nasal aerosol, Qutenza (capsaicin), Ragwitek (ShortRagweed Pollen Allergen Extract), Rapamune (sirolimus) oral solution,Rapamune (sirolimus) Tablets, Rayos (prednisone) delayed-releasetablets, Rebetol (ribavirin), REBETRON™ Combination Therapy, Relenza,Rescriptor Tablets (delavirdine mesylate tablets), RespiGam (RespiratorySyncitial Virus Immune Globulin Intravenous), Restasis (cyclosporineophthalmic emulsion), Reyataz (atazanavir sulfate), Rid Mousse, Rotarix(Rotavirus Vaccine, Live, Oral), Rotateq (rotavirus vaccine, live oralpentavalent), Selzentry (maraviroc), Simponi (golimumab), Simulect,Sitavig (acyclovir) buccal tablets, Spectracef, SPORANOX (itraconazole),Stribild (elvitegravir, cobicistat, emtricitabine, tenofovir disoproxilfumarate), Stromectol (ivermectin), Sustiva, Sylvant (siltuximab),Synercid I.V., Taltz (ixekizumab), Tamiflu capsule, Taxol, Tecfidera(dimethyl fumarate), Teflaro (ceftaroline fosamil), Timentin, Tindamax,tinidazole, Tivicay (dolutegravir), Tri-Nasal Spray (triamcinoloneacetonide spray), Triumeq (abacavir, dolutegravir, and lamivudine),Trivagizole 3 (clotrimazole) Vaginal Cream, Trizivir (abacavir sulfate;lamivudine; zidovudine AZT) Tablet, Trovan, Tudorza Pressair (aclidiniumbromide inhalation powder), Twinrix, Tygacil (tigecycline), Tysabri(natalizumab), Tyzeka (telbivudine), Valcyte (valganciclovir HCl),Valtrex (valacyclovir HCl), VariZIG, Varicella Zoster Immune Globulin(Human), Veramyst (fluticasone furoate), Veregen (kunecatechins), Vfend(voriconazole), Vibativ (telavancin), Victrelis (boceprevir), Videx(didanosine), VIRACEPT (nelfinavir mesylate), Viramune (nevirapine),Viread (tenofovir disoproxil fumarate), Viread (tenofovir disoproxilfumarate), Viroptic, Vistide (cidofovir), Vitrasert Implant, Xifaxan(rifaximin), Xigris (drotrecogin alfa [activated]), Xyzal(levocetirizine dihydrochloride), Zerit (stavudine), Zirgan (ganciclovirophthalmic gel), Zithromax (azithromycin), Zortress (everolimus),Zymaxid (gatifloxacin ophthalmic solution), Zyrtec (cetirizine HCl).

In one embodiment, the second agent is metabolism-modulating orcachexia-modulating drug, e.g. Accretropin (somatropin rDNA Original),ACTOplus met (pioglitazone hydrochloride and metformin hydrochloride),ACTOS, Afrezza (insulin human) Inhalation Powder, Amaryl (Glimepiride),Avandamet (rosiglitazone maleate and metformin HCl), Avandia(rosiglitazone maleate), Belviq (lorcaserin hydrochloride), Bydureon(exenatide extended-release for injectable suspension), Byetta(exenatide), Cernevit, Cycloset, bromocriptine mesylate, DesmopressinAcetate (DDAVP), Farxiga (dapagliflozin) Genotropin (somatropin)injection, Genotropin (somatropin) lyophilized powder, Geref (sermorelinacetate for injection), Glipizide Tablets, Glucagon, Glyburide Tablets,Glyset (miglitol), Humalog (insulin lispro), Increlex (mecasermin),Invokana (canagliflozin), Januvia (sitagliptin phosphate), Jardiance(empagliflozin), Jentadueto (linagliptin plus metformin hydrochloride),Juvisync (sitagliptin and simvastatin), Lantus (insulin glargine [rDNAorigin] injection), Metaglip (glipizide/metformin HCl), Nesina(alogliptin), NovoLog (insulin aspart), Novolog Mix 70/30, Nutropin(somatropin-rDNA origin), Onglyza (saxagliptin), Prandin, Precose(acarbose), Symlin (pramlintide), Synjardy (empagliflozin and metforminhydrochloride), Tanzeum (albiglutide), Tradjenta (linagliptin), Tresiba(insulin degludec injection), Trulicity (dulaglutide), Victoza(liraglutide), Xigduo XR (dapagliflozin+metformin hydrochloride),Progestagens: megestrol acetate/Medroxyprogesterone acetate,Corticosteroids, Omega-3 fatty acids—EPA, Cannabinoids (dronabinol),Bortezomib, Thalidomide, Ghrelin, COX-2 inhibitors, Insulin, BCAA,Oxandrolone, Melanocortin antagonists, (32 agonists (formoterol),Anti-myostatin peptibody, Anti-IL-6, SARMs, Oxandrolone, Olanzapine,anti-IL-6 antibodies, Anamorelin, AndroGel transdermal, Testopelimplant, Testim transdermal, testosterone cypionate intramuscular,Androderm transdermal, Axiron transdermal, Fortesta transdermal,megestrol oral, Megace oral, Depo-Testosterone intramuscular, Megace ESoral, testosterone enanthate intramuscular, testosterone transdermal,Striant buccal, Humatrope injection, Nutropin AQ subcutaneous, Omnitropesubcutaneous, Natesto nasal, Saizen subcutaneous, Genotropin Miniquicksubcutaneous, Android oral, Aveed intramuscular, somatropin injection,testosterone implant, Genotropin subcutaneous, Norditropin FlexProsubcutaneous, methyltestosterone oral, testosterone undecanoateintramuscular, Vogelxo transdermal, somatropin subcutaneous, Testredoral, Methitest oral, testosterone buccal, testosterone nasal, TestoneCIK intramuscular, Serostim subcutaneous, Zorbtive subcutaneous, Saizensubcutaneous, Nutropin AQ Nuspin subcutaneous, Zomacton subcutaneous.

In one embodiment, the second agent is a therapeutic agent which is anon-drug treatment. For example, the second therapeutic agent isradiation therapy, cryotherapy, hyperthermia and/or surgical excision oftumor tissue.

In some embodiments, the subject is treated with a glycan therapeuticdescribed herein in combination with two or more other pharmaceuticalagents, e.g., two or more (e.g., 3 or more, 4 or more) chemotherapeuticagents, or a combination of different classes of therapeutic agentsdescribed herein. For example, a cancer subject may be treated with aglycan therapeutic described herein in combination with radiationtherapy, a chemotherapeutic cocktail of 2, 3, 4 or more drugs, andoptionally also in combination with a checkpoint inhibitor or a celltherapy (e.g., T cell therapy).

If determined useful by a treating physician or other healthcareprovider, the pharmaceutical glycan therapeutic compositions describedherein can be administered in combination with various other standard ofcare therapies. In some embodiments, the combination of administrationof the glycan therapeutic and the standard-of-care therapy agent (e.g.,an anti-cancer drug) has additive or synergistic treatment effects. Thepharmaceutical glycan therapeutic compositions may be administered priorto, concurrent with, or post treatment with standard of care therapies.

In some instances, the therapies, e.g., treatment with cytotoxic oranti-microbial drugs disrupt the composition or health of the GI tract'shost cells and microbiota or that of non-GI sites. In one embodiment,the disruption by the drugs leads to the undesirable proliferation ofharmful bacteria or pathogens. In some embodiments, the disruption ofthe host cells and/or microbiota by the drugs causes one or more of thesymptoms described herein. In some embodiments, administration of thepharmaceutical glycan therapeutic compositions described herein isuseful for alleviating those symptoms. In some embodiments,administration of the pharmaceutical glycan therapeutic compositionimproves the composition of the gastrointestinal or non-gut microbialcommunity and host cells (e.g., modulates shifts in the composition orfunction of the microbiota that decrease the intensity or duration ofthe symptoms).

Provided herein are methods of treating an immune imbalance in asubject. Provided herein is a method of treating an immune imbalance ina human subject, comprising: administering to the subject apharmaceutical composition, a medical food or a dietary supplementcomprising a glycan therapeutic preparation, in an effective amount totreat the subject. Optionally, a second agent may be administered. Themethods also include methods for reducing an infection and/or aninflammation in a subject having an immune imbalance. Also provided aremethods of modulating the composition and/or metabolic activity of theintestinal bacterial community of a subject having an immune imbalance,and methods of modulating one or more functional pathways in a subjecthaving an immune imbalance. Further, methods of treating a dysbiosis ina subject having an immune imbalance are provided. In some embodiments,the immune imbalance results in or is associated with a cancer.

In some embodiments, immune suppression and/or insufficient immuneinflammatory activation is characterized by the overgrowth of pathogeniccells. Examples of pathogenic cells include intracellular pathogens,extracellular pathogens, viruses, and cancerous cells. Immunesuppression and/or insufficient immune inflammatory activation, in someembodiments, is associated with tolerance, e.g., resulting from animbalance in the ratio of tolerogenic cell subsets (e.g. regulatory Tcells) or activities (e.g. tolerogenic cytokine secretion such IL-10,TGF-beta) to inflammatory cell subsets (e.g. Th1 cells) or activities(e.g. inflammatory cytokine secretion such as TNF-alpha, IL-17), withthe tolerogenic functions displaying higher activity than theinflammatory functions. Immune suppression and/or insufficient immuneinflammatory activation, in some embodiments, is associated with theimmune system not recognizing the pathogenic cell as a pathogen, whichfrequently occurs in the case of cancerous cells.

Aberrant immune inflammatory activation, in some embodiments, ischaracterized by damage to or a decrease in the proliferation ofnon-pathogenic cells. Examples of non-pathogenic cells are any cells orcell-structures (including tissues and organs) that are not-targeted bythe immune system for attack in a healthy individual. For example, theepithelium of the gastrointestinal tract is not substantially damaged bythe immune system in healthy individuals but is damaged by the immunesystem in individuals with inflammatory diseases such as, e.g.,inflammatory bowel disease. For example, the pancreas is notsubstantially targeted by the inflammatory arm of the immune system inpatients who do not have autoimmune diabetes, but is targeted inpatients with type-1 diabetes. Aberrant immune inflammatory activation,in some embodiments, is associated with an imbalance in the ratio oftolerogenic cell subsets (e.g. regulatory T cells) or activities (e.g.tolerogenic cytokine secretion such IL-10, TGF-beta) to inflammatorycell subsets (e.g. Th1 cells) or activities (e.g. inflammatory cytokinesecretion such as TNF-alpha, IL-17), with the inflammatory functionsdisplaying higher activity than the tolerogenic functions.

Examples of immune imbalances include: Clostridium difficile infection(CDI); Vancomycin-resistant enterococci (VRE) infection, infectiouscolitis, and C. difficile colitis; mycoses, such as, e.g., Candidaalbicans infection, Campylobacter jejuni infection, Helicobacter pyloriinfection; diarrhea, such as, e.g., Clostridium difficile associateddiarrhea (CDAD), antibiotic-associated diarrhea (AAD),antibiotic-induced diarrhea, travellers' diarrhea (TD), pediatricdiarrhea, (acute) infectious diarrhea, colon and liver cancers, ameboma;necrotizing enterocolitis (NEC), and small intestine bacterialovergrowth (SIBO); indigestion or non-ulcer dyspepsia; anal fissures,perianal abscess and anal fistula; diverticulosis or diverticulitis;peptic ulcers; and gastroenteritis. Cancers that are solid or liquidcancer and includes benign or malignant tumors, and hyperplasias,including gastrointestinal cancer (such as non-metastatic or metastaticcolorectal cancer, pancreatic cancer, gastric cancer, oesophagealcancer, hepatocellular cancer, cholangiocellular cancer, oral cancer,lip cancer); urogenital cancer (such as hormone sensitive or hormonerefractory prostate cancer, renal cell cancer, bladder cancer, penilecancer); gynecological cancer (such as ovarian cancer, cervical cancer,endometrial cancer); lung cancer (such as small-cell lung cancer andnon-small-cell lung cancer); head and neck cancer (e.g. head and necksquamous cell cancer); CNS cancer including malignant glioma,astrocytomas, retinoblastomas and brain metastases; malignantmesothelioma; non-metastatic or metastatic breast cancer (e.g. hormonerefractory metastatic breast cancer); skin cancer (such as malignantmelanoma, basal and squamous cell skin cancers, Merkel Cell Carcinoma,lymphoma of the skin, Kaposi Sarcoma); thyroid cancer; bone and softtissue sarcoma; and haematologic neoplasias (such as multiple myeloma,acute myelogenous leukemia, chronic myelogenous leukemia,myelodysplastic syndrome, acute lymphoblastic leukemia, Hodgkin'slymphoma).

Other examples of immune imbalances include: Gastrointestinalinflammatory diseases including inflammatory bowel disease (IBD),ulcerative colitis (UC), Crohn's disease (CD), idiopathic inflammationof the small bowel, indeterminatal colitis, pouchitis; irritable bowelsyndrome (IBS), colon and liver cancers, necrotizing enterocolitis(NEC), intestinal inflammation, constipation, microscopic colitis,diarrhea; graft versus host disease (GVHD); (food) allergies;pseudomembranous colitis; indigestion or non-ulcer dyspepsia;diverticulosis or diverticulitis, ischemic colitis; radiation colitis orenteritis; collagenous colitis; gastroenteritis; and polyps.atopicdermatitis, asthma, multiple sclerosis, immune-mediated or Type Idiabetes mellitus, systemic lupus erythematosus, psoriasis, scleroderma,autoimmune thyroid disease, alopecia greata, Grave's disease,Guillain-Barré syndrome, celiac disease, Sjögren's syndrome, rheumaticfever, gastritis, autoimmune atrophic gastritis, autoimmune hepatitis,insulitis, oophoritis, orchitis, uveitis, phacogenic uveitis, myastheniagravis, primary myxoedema, pernicious anemia, autoimmune haemolyticanemia, Addison's disease, scleroderma, Goodpasture's syndrome,nephritis, for example, glomerulonephritis, psoriasis, pemphigusvulgaris, pemphigoid, sympathetic opthalmia, idiopathic thrombocylopenicpurpura, idiopathic feucopenia, Wegener's granulomatosis andpoly/dermatomyositis.

Provided herein are methods of treating a nutritional imbalance in asubject. Provided herein is a method of treating a nutritional imbalancein a human subject, comprising: administering to the subject apharmaceutical composition, a medical food or a dietary supplementcomprising a glycan therapeutic preparation, in an effective amount totreat the subject. Optionally, a second agent may be administered. Themethods also include methods for reducing an infection and/or aninflammation in a subject having a nutritional imbalance. Also providedare methods of modulating the composition and/or metabolic activity ofthe intestinal bacterial community of a subject having a nutritionalimbalance, and methods of modulating one or more functional pathways ina subject having a nutritional imbalance. Further, methods of treating adysbiosis in a subject having a nutritional imbalance are provided. Insome embodiments, the nutritional imbalance results in or is associatedwith a cancer.

In some embodiments, the nutritional imbalances is associated with anaberrant inflammatory immune activation that alters metabolichomeostasis. In some embodiments, the nutritional imbalance isassociated with an imbalance in the ratio of tolerogenic cell subsets(e.g. regulatory t cells) or activities (e.g. tolerogenic cytokinesecretion such IL-10, TGF-beta) to inflammatory cell subsets (e.g. Th1cells) or activities (e.g. inflammatory cytokine secretion such asTNF-alpha, IL-17), with the inflammatory functions displaying higheractivity than the tolerogenic functions. In some embodiments, anincreased immune in inflammatory activity affects the mechanisms thatmetabolic organs and systems utilize for communication. For example,cancer patients who have malnutrition often exhibit a high level ofleptin, which is a hormone that induces satiety and thus decreases thepatient's hunger. Other diseases that lead to cachexia include, e.g.chronic obstructive pulmonary disease (COPD), rheumatoid arthritis,chronic infection or sepsis, renal failure, heart failure and cancer.The condition is characterized by inflammation, anorexia, insulinresistance and increased muscle protein breakdown with or without a lossof fat mass.

Examples of nutritional imbalance include: Cachexia, anorexia nervosa,kwashiorkor and marasmus. Diseases that lead to cachexia include, e.g.chronic obstructive pulmonary disease (COPD), rheumatoid arthritis,chronic infection or sepsis, renal failure, heart failure and cancer.The condition is characterized by inflammation, anorexia, insulinresistance and increased muscle protein breakdown with or without a lossof fat mass.

Drug- or Treatment-Induced Toxicities

Provided herein are methods of reducing drug- or treatment-inducedsymptoms in a human subject, e.g. a subject undergoing anti-cancertreatment (being treated with an anti-cancer agent), and subjects intreatment for or having an immune imbalance or a nutritional imbalance.Such drug- or treatment-induced symptoms include any toxicity, digestiveabnormalities or gastrointestinal distress. Provided herein are methodsfor preventing, treating or alleviating the symptoms of variousgastrointestinal ailments by administering the glycan therapeuticcompositions described herein. The method include administering to thehuman subject a pharmaceutical composition comprising a glycantherapeutic preparation in an amount effective to reduce one or moresymptoms induced by a drug or treatment. In one embodiment, thetreatment is radiation treatment, cryotherapy, hyperthermia or surgicalexcision of tumor tissue. Exemplary toxicities or digestive abnormalies(gastrointestinal distress) include weight-gain, constipation,heartburn, upset stomach, gas, bloating, flatulence, diarrhea, abdominalpain, cramping, nausea, and vomiting. In some embodiments, the digestiveabnormality is diarrhea. In some embodiments, the digestive abnormalityis constipation.

Other examples include treatment (or toxicity) associated symptoms suchas gas, heartburn, stomach upset, bloating, flatulence, diarrhea,abdominal pain, cramping, nausea, or vomiting. Minor digestive problemsrelated to the GI also include occasional bloating, diarrhea,constipation, gas, or stomach upset.

If desired, the glycan therapeutic compositions described herein can beadministered in combination with various therapies that are associatedwith gastrointestinal distress. Such therapies include, withoutlimitation, radiation and chemotherapy for cancers, and antibiotictherapy for various microbial maladies. In some embodiments, thetherapies disrupt the composition and health of the intestine's normalmicrobiota. In some instances, the disruption leads to the undesirableproliferation of harmful bacteria and accompanying symptoms describedherein. Administration of the glycan therapeutic compositions describedherein is useful for treating those symptoms.

The glycan therapeutic compositions described herein are suitable foradministration to humans in need thereof. In certain embodiments, thesubject is a human who has one or more symptoms of a disturbed gutmicrobiota. In some embodiments, the disturbance can be rectified by theuse of the glycan therapeutics described herein so that normalphysiological growth and function of both the commensal microbiota andthe host can be achieved.

In some embodiments, the glycan therapeutics described herein may beused in combination with one or more of: a pain-management drug (e.g.,opioids) an antidepressant, an antiepileptic, a steroid, a drug formanaging a GI tract motility disorder, an anti-inflammatory agent (e.g.,NSAID), and an antimicrobial agent (e.g., antibiotic), describedelsewhere herein, to treat any toxicity, digestive abnormalies and othergastrointestinal distress associated with administration of the drugs toa subject.

Other examples of drugs which often are associated with drug- ortreatment-induced (toxicity) symptoms include, a cancer drug, ananti-diabetic, an immune-suppressive drug, an antimicrobial drug, achemotherapeutic, an anti-psychotic, a proton pump inhibitor, and anon-steroid anti-inflammatory drug (NSAID).

In some embodiments, the glycan therapeutics described herein may beused in combination with one or more anti-cancer agents, including,checkpoint modulators, cell therapies, cancer vaccines, chemotherapeuticagents, and biologics, described elsewhere herein, to treat toxicities,digestive abnormalies and other gastrointestinal distress associatedwith administration of the drugs to a subject.

Provided herein are methods of lowering or reducing the number orintensity of an unwanted side effect of a treatment or therapy, such as,e.g., an anti-cancer treatment or therapy (and treatments or therapiesrelating to immune imbalances or nutritional imbalances), in a subject,comprising a) administering a pharmaceutical composition comprising aglycan therapeutic preparation described herein to a subject who hasreceived the treatment or therapy; b) administering the treatment ortherapy to a subject who has been treated with a pharmaceuticalcomposition comprising a glycan therapeutic preparation; or c)administering a pharmaceutical composition comprising a glycantherapeutic preparation and administering the treatment or therapy, to asubject, thereby decreasing the side effect of the treatment or therapyin the subject. In some embodiments, the onset of the side effect isprior to administration of the glycan therapeutic preparation. In someembodiments, the glycan therapeutic preparation is administered afteronset of the side effect. In some embodiments, the side effect of thetreatment or therapy results in an unwanted symptom. In someembodiments, the unwanted side effect is a gastrointestinal side effect,such as a digestive abnormality. In some embodiments, the unwanted sideeffect is a non-gastrointestinal side effect, such as, e.g., anxiety,fear, depression, mental fog, dermatitis, chest pain, shortness ofbreath, weight gain, weight loss, etc.

In some embodiments, the unwanted side effect is one or more of:abdominal pain, cramping, nausea, or vomiting, upset stomach, gas,bloating, flatulence, diarrhea, constipation, heartburn, mucositis,weight loss, and weight-gain.

In some embodiments, the unwanted side effect is associated withanti-cancer treatment (or treatments for an immune imbalance or anutritional imbalance). In some embodiments, the unwanted side effectsrelated to anti-cancer treatment include one or more of: radiationinjury pain, surgical pain, phantom pain, acute pain, chronic orpersistent pain, breakthrough pain, peripheral neuropathy, stomatitis,mucositis, nausea, vomiting, diarrhea (acute, chronic), constipation(acute, chronic), urinary incontinence, fatigue (acute or chronic),anemia, lymphedema, infections, anxiety, fear, depression, fertilitydefects, and risk of developing a second cancer. In some embodiments,the unwanted side effects related to anti-cancer treatment includeinfections, such as bacterial infections, including: Pseudomonasaeruginosa, Klebsiella pneumonia, Escherichia coli, Salmonella,Clostridium difficile, Staphylococcus aureus, Staphylococcus epidemidis,Streptococcus viridians, Pneumococcus, Enterococcus; viral infections,including: Varicella zoster virus (VZV), Herpes simplex virus (HSV),Cytomegalovirus (CMV), hepatitis viruses, respiratory viruses (e.g.,influenza, respiratory syncytial virus (RSV)); protozoal infections,including: Toxoplasma gondii, and Cryptosporidium; and fungalinfections, including: Pneumocystis jirovecii, Candida, Aspergillus,Cryptococcus, Histoplasma, Coccidioides.

In some embodiments, the unwanted side effects related to anti-cancertreatment include malnutrition and cachexia (wasting syndrome).

In some embodiments, the unwanted side effect related to anti-cancertreatment is mucositis, including mucosal tissue ulceration andinfection. In some embodiments, the unwanted side effect related toanti-cancer treatment (such as, e.g., chemotherapy and radiation) isoral mucositis.

In some embodiments, the one or more unwanted side effects aredose-limiting, e.g., they require a reduction in subsequent therapeuticdoses (e.g. for chemotherapy). Dose limiting toxicity prevents subjectsfrom being treated with the maximal efficacious dose of a drug.

In some embodiments, the methods further comprise administering apharmaceutical composition comprising a glycan therapeutic preparationto a subject who has received a first treatment (e.g. an anti-cancerdrug treatment or anti-cancer therapy), and optionally, providing asecond treatment, e.g., wherein the second treatment comprisesadministration of the drug or therapy at a higher dosage, at morefrequent intervals, at a higher total of individual administrations,providing a higher Cmax, providing a higher trough level, etc., than theprior treatment.

In some embodiments, the methods further comprise providing a subsequenttreatment (e.g. an anti-cancer drug treatment or anti-cancer therapy) toa subject who has received a pharmaceutical composition comprising aglycan therapeutic preparation and received the first treatment, whereinthe second treatment comprises administration of the drug or therapy ata higher dosage, at more frequent intervals, at a higher total ofindividual administrations, providing a higher Cmax, providing a highertrough level, etc., than the prior treatment.

In one embodiment, the subject being identified to be suitable fortreatment with a glycan therapeutic has, is suspected of having or issuspected of developing drug-induced diarrhea (such as, e.g.,5-fluorouracil (5-FU), methotrexate, irinotecan, taxanes, monoclonalantibodies and hormonal agents). In one embodiment, the subject beingidentified to be suitable for treatment with a glycan therapeutic has,is suspected of having or is suspected of developing drug-inducedconstipation (such as, e.g., vinca alkaloids, platinums (e.g.,cisplatin), thalidomide and hormonal agents). In one embodiment, thesubject being identified to be suitable for treatment with a glycantherapeutic has, is suspected of having or is suspected of developing adrug-induced toxicity. In one embodiment, the subject being identifiedto be suitable for treatment with a glycan therapeutic has, is suspectedof having or is suspected of developing chemotherapy-induced mucositis.In one embodiment, the subject being identified to be suitable fortreatment with a glycan therapeutic has, is suspected of having or issuspected of developing a drug-induced intolerance (e.g. tochemotherapies). In one embodiment, the subject being identified to besuitable for treatment with a glycan therapeutic has, is suspected ofhaving or is suspected of developing cachexia (wasting syndrome). In oneembodiment, the subject being identified to be suitable for treatmentwith a glycan therapeutic has, is suspected of having or is suspected ofdeveloping drug-induced microbiome damage, drug-induced microbiomedisease, drug-induced gastrointestinal disease, drug-induced enteritisor colitis or similar drug-induced disorder or condition.

In some embodiments, the pharmaceutical composition comprising a glycantherapeutic preparation is administered prior to, concomitant with orafter administration of the (e.g. anti-cancer) drug or non-drug (e.g.,anti-cancer) treatment, administration of which induces the symptoms.

In some embodiments, administration of a drug is associated withdysbioses that can, e.g., occur during the treatment regimen. In someembodiments, the dysbiosis causes or amplifies the drug- ortreatment-induced symptoms, such as toxicities, including digestiveabnormalities. In some embodiments, administration of the glycantherapeutic modulates the microbiome such that the drug- ortreatment-induced symptoms are reduced. In some embodiments, the glycantherapeutic promotes the growth of commensal bacteria and/or supportsthe growth of beneficial microbial communities which would negatively beaffected or lost in response to the drug treatment or which cancomplement commensal bacteria that have been negatively affected or lostin response to the drug treatment.

Provided herein are methods of treating a dysbiosis in a subjectcomprising administering to the subject a pharmaceutical compositioncomprising a glycan therapeutic preparation thereby treating thedysbiosis. The dysbiosis, in some embodiments, is concurrent with (orthe result of) a disease, disorder or condition, such as, e.g., animmune imbalance, a nutritional imbalance and/or cancer. In someembodiments, the dysbiosis is concurrent with (or the result of) atreatment or therapy, e.g., anti-cancer therapy, pain management, etc.

In some embodiments, the unwanted side effects, including toxicitiessuch as digestive abnormalities, are associated with treatment of thesubject with a chemotherapeutic agent. In one embodiment, the digestiveabnormality is diarrhea. In specific embodiments, the chemotherapeuticagent is Irinotecan, 5-fluorouracil, leucovorin, or combinationsthereof. In specific embodiments, the chemotherapeutic agent isoxaliplatin, leucovorin, 5-fluorouracil, or combinations thereof. Inspecific embodiments the chemotherapeutic agent is bortezomib, imatinib,lenalidomide, imbruvica, ipilimumab, pertuzumab, capecitabine,docetaxel, lapatinib, erlotinib, or combinations thereof. In someembodiments, the chemotherapeutic agent is Carmustine, Etoposide,Aracytine, Melphalan, or combinations thereof. In specific embodimentsthe chemotherapeutic agent is cytarabine, daunorubicine, etoposide, orcombinations thereof. In specific embodiments the chemotherapeutic agentis amsacrine, cytarabine, etoposide, or combinations thereof. Inspecific embodiments, the chemotherapeutic agent is mitoxantrone,cytarabine, or combinations thereof.

In some embodiments, the unwanted side effects, including toxicitiessuch as digestive abnormalities, are associated with treatment of thesubject with an antibiotic. In one embodiment, the digestive abnormalityis diarrhea. In specific embodiments, the antibiotic is ciprofloxacin,clindamycin, amoxicillin-clavulanate, cefixime, ephalosporins,fluoroquinolones, azithromycin, clarithromycin, erythromycin,tetracycline, or azithromycin.

In some embodiments, the unwanted side effects, including toxicitiessuch as digestive abnormalities, are associated with treatment of thesubject with an anti-psychotic drug. In one embodiment, the digestiveabnormality is weight gain. In one embodiment, the drug is olanzapine.

In some embodiments, the unwanted side effects, including toxicitiessuch as digestive abnormalities, are associated with treatment of thesubject with a proton-pump inhibitor drug. In one embodiment, thedigestive abnormality is diarrhea. In specific embodiments, the drug isranitidine, famotidine, cimetidine, omeprazole, sucralfate, oresomeprazole.

In some embodiments, the unwanted side effects, including toxicitiessuch as digestive abnormalities, are associated with treatment of thesubject with a non-steroidal anti-inflammatory drug (NSAID). In oneembodiment, the digestive abnormality is diarrhea. In specificembodiments, the drug is naproxen, diclofenac, indomethacin, ibuprofen,ketoprofen, piroxicam, celecoxib, nimesulid, or aspirin.

In some embodiments, the unwanted side effects, including toxicitiessuch as digestive abnormalities, are associated with treatment of thesubject with metformin, paroxetine, valproic acid, or clozapine.

In one embodiment, reducing the one or more symptoms (e.g., of unwantedside effects) increases compliance by the subject to the treatmentregimen. In one embodiment, reducing one or more symptom (e.g., ofunwanted side effects) enables the physician to prescribe a higher-doseof the drug to be administered. In such embodiments, treatment of theunderlying disease is more effective (e.g. increased reduction ofdisease symptoms, shorter period to achieve a disease or symptom-freestate, or longer maintainance of a disease or symptom-free state, etc.).

In one embodiment, a method of lowering toxicity of a drug treatment(e.g., an anti-cancer drug treatment) in a subject is provided. Themethod includes: a) administering a pharmaceutical compositioncomprising a glycan therapeutic preparation to a subject who hasreceived the drug treatment; b) administering the drug treatment to asubject who has been treated with a pharmaceutical compositioncomprising a glycan therapeutic preparation; or c) administering apharmaceutical composition comprising a glycan therapeutic preparationand administering the drug treatment, to a subject, thereby treating thesubject. In some embodiments, the toxicity is dose-limiting toxicity. Insome embodiments, the method increases the tolerance of the subject todrug treatment, e.g. an anti-cancer drug treatment.

In some embodiments, dose limiting toxicity prevents subjects from beingtreated with the maximal efficacious dose of a drug. As one example ofdose-limiting toxicity, diarrhea can be caused by the chemotherapy drugsirinotecan and 5-fluoruracil. Irinotecan and 5-fluorouracil may damagethe intestinal epithelium of subjects. As a result nutrient and fluidabsorption and secretion is modulated. In some instances, the digestiveabnormality forces a clinician to reduce the dose of the drug to adjustit to the subject's tolerance level. In some instances, the lowering maylead to a treatment regimen with a less efficacious dose therebylimiting the treatment effect (or prolonging the treatment interval. Insome embodiments, glycan therapeutic preparations are administered totreat dose limiting toxicity, e.g., to increase the dose that istolerated by the subject. In some embodiments, tolerability is increasedby limiting one or more digestive abnormalities associated with therespective efficacious drug dose.

Other Embodiments

In some embodiments, the subject experiences a reduction in at least onesymptom of the gastrointestinal disease, disorder or condition followingtreatment. In some embodiments, a reduction in the severity of a symptomfollowing treatment can be determined (e.g. by measuring a knownbiomarker) and is in the order of about 3%, 5%, 7%, 10%, 20%, 30%, 40%,50%, 60%, 70%, 80%, 90%, 95%, or about 100%. In some embodiments, thesymptoms, measured as described herein, are decreased by an average ofabout 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or about 100%when compared to symptoms prior to the administration of apharmaceutical glycan therapeutic composition. In some embodiments, thereduction in the severity of the symptom persists for at least about aday, two days, three days, four days, five days, a week, two weeks,three weeks, a month, 3 months, 6 months, 9 months, a year, two years,five years, ten years after treatment or the reduction is permanent.

In one embodiment, a symptom of a gastrointestinal disease, disorder orcondition remains partially, substantially, or completely eliminated ordecreased in severity in a subject for at least about 1 day, 1 week, 1month, 2 months, 3 months, 4 months, 5 months, 6 months, 9 months, oneyear, 18 months, two years, three years, four years, five years, tenyears, or more than ten years after the termination of treatment. Inanother embodiment a symptom of a gastrointestinal disease, disorder orcondition is permanently eliminated or decreased in severity in asubject after the termination of treatment.

Proteomic Analysis of Microbial Populations

Preparations of glycan therapeutics may be selected based on theirability to increase the expression of microbial proteins associated withhealthy states or to decrease the expression of microbial proteinsassociated with diseased states. Proteomic analysis of microbialpopulations can be performed following protocols known to one skilled inthe art (e.g., Cordwell, Exploring and exploiting bacterial proteomes,Methods in Molecular Biology, 2004, 266: 115). To identifydifferentially expressed proteins (for example, to identify changes inprotein expression upon treatment of microbial populations with glycantherapeutics), proteomic analysis can be performed as described, e.g.,in Juste et al. (Bacterial protein signals are associated with Crohn'sdisease, Gut, 2014, 63: 1566). For example, the protein is isolated fromthe microbial lysates of two samples (for example, an untreatedmicrobial population and a population that has been treated with glycantherapeutics). Each protein sample is labeled (e.g., with a fluorescentdye, e.g., Cy3 or Cy5 CyDye DIGE Fluor minimal dye, GE Healthcare) andanalyzed by two-dimensional differential gel electrophoresis (2D-DIGE).Gels are stained and protein spots identified as being significantlydifferent between the two samples are excised, digested, and analyzed byliquid chromatography-tandem spectrometry (LC-MS/MS). X!TandemPipelinemay be used to identify differentially expressed proteins.

Preparations of glycan therapeutics may also be selected foradministration to a human subject based on their effect on the presenceof microbial fermentation products. For example, preparations of glycantherapeutics can be selected for their ability to induce or promotegrowth of bacteria that produce short chain fatty acids such aspropionate (propionic acid), acetate, and/or butyrate (butyric acid).Similarly, preparations of glycan therapeutics can be selected for theirability to induce or promote growth of bacteria that produce lacticacid, which can modulate the growth of other bacteria by producing anacidic environment. Such analysis may also be used to pair probioticbacteria with glycan therapeutics such that the glycan therapeutic is asubstrate for the production of the desired fermentation products.

The metabolites that are present in fresh or spent culture media or inbiological samples collected from human subjects may be determined usingmethods known in the art and described herein. Unbiased methods that maybe used to determine the relative concentration of metabolites in asample and are known to one skilled in the art, such as gas or liquidchromatography combined with mass spectrometry or ¹H-NMR. Thesemeasurements may be validated by running metabolite standards throughthe same analytical systems.

In the case of gas chromatography-mass spectrometry (GC-MS) orliquid-chromatography-mass spectrometry (LC-MS) analysis, polarmetabolites and fatty acids can be extracted using monophasic orbiphasic systems of organic solvents and an aqueous sample andderivatized (Fendt et al., Reductive glutamine metabolism is a functionof the α-ketoglutarate to citrate ratio in cells, Nat Commun, 2013,4:2236; Fendt et al., Metformin decreases glucose oxidation andincreases the dependency of prostate cancer cells on reductive glutaminemetabolism, Cancer Res, 2013, 73:4429; Metallo et al., Reductiveglutamine metabolism by IDH1 mediates lipogenesis under hypoxia, Nature,2011, 481:380). An exemplary protocol for derivatization of polarmetabolites involves formation of methoxime-tBDMS derivatives throughincubation of the metabolites with 2% methoxylamine hydrochloride inpyridine followed by addition ofN-tert-butyldimethylsilyl-N-methyltrifluoroacetamide (MTBSTFA) with 1%tert-butyldimethylchlorosilane (t-BDMCS). Non-polar fractions, includingtriacylglycerides and phospholipids, may be saponified to free fattyacids and esterified to form fatty acid methyl esters, for example,either by incubation with 2% H₂SO₄ in methanol or by using Methyl-8reagent (Thermo Scientific). Derivatized samples may then be analyzed byGC-MS using standard LC-MS methods, for example, a DB-35MS column (30m×0.25 mm i.d.×0.25 μm, Agilent J&W Scientific) installed on a gaschromatograph (GC) interfaced with an mass spectrometer (MS). Massisotopomer distributions may be determined by integrating metabolite ionfragments and corrected for natural abundance using standard algorithms,such as those adapted from Fernandez et al. (Fernandez et al.,Correction of 13C mass isotopomer distributions for natural stableisotope abundance, J Mass Spectrom, 1996, 31:255). In the case of liquidchromatography-mass spectrometry (LC-MS), polar metabolites may beanalyzed using a standard benchtop LC-MS/MS equipped with a column, suchas a SeQuant ZIC-pHILIC Polymeric column (2.1×150 mm; EMD Millipore).Exemplary mobile phases used for separation could include buffers andorganic solvents adjusted to a specific pH value. In combination or inthe alternative, extracted samples may be analyzed by ¹H-nuclearmagnetic resonance (¹H-NMR). Samples may be combined with isotopicallyenriched solvents such as D2O, optionally in the presence of a bufferedsolution (e.g., Na₂HPO₄, NaH₂PO₄ in D2O, pH 7.4). Samples may also besupplemented with a reference standard for calibration and chemicalshift determination (e.g., 5 mM 2,2-dimethyl-2-silapentane-5-sulfonatesodium salt (DSS-d₆, Isotec, USA)). Prior to analysis, the solution maybe filtered or centrifuged to remove any sediment or precipitates, andthen transferred to a suitable NMR tube or vessel for analysis (e.g., a5 mm NMR tube). ¹H-NMR spectra may be acquired on a standard NMRspectrometer, such as an Avance II+500 Bruker spectrometer (500 MHz)(Bruker, DE), equipped with a 5 mm QXI-Z C/N/P probe-head) and analyzedwith spectra integration software (such as Chenomx NMR Suite 7.1;Chenomx Inc., Edmonton, AB). (Duarte et al., ¹H-NMR protocol forexometabolome analysis of cultured mammalian cells, Methods Mol Biol,2014:237-47). Alternatively, ¹H-NMR may be performed following otherpublished protocols known in the art (Chassaing et al., Lack of solublefiber drives diet-induced adiposity in mice, Am J Physiol GastrointestLiver Physiol, 2015; Bal et al., Comparison of Storage Conditions forHuman Vaginal Microbiome Studies, PLoS ONE, 2012:e36934).

All publications, patents, and patent applications cited or referencedin this specification are herein incorporated by reference to the sameextent as if each independent publication or patent publication wasspecifically and individually indicated to be incorporated by reference.

EXAMPLES

The invention is further illustrated by the following examples. Theexamples are provided for illustrative purposes only, and are not to beconstrued as limiting the scope or content of the invention in any way.The practice of the present invention will employ, unless otherwiseindicated, conventional methods of protein chemistry, biochemistry,recombinant DNA techniques and pharmacology, within the skill of theart. Such techniques are explained fully in the literature. See, e.g, T.E. Creighton, Proteins: Structures and Molecular Properties (W.H.Freeman and Company, 1993); Green & Sambrook et al., Molecular Cloning:A Laboratory Manual, 4th Edition (Cold Spring Harbor Laboratory Press,2012); Colowick & Kaplan, Methods In Enzymology (Academic Press);Remington: The Science and Practice of Pharmacy, 22nd Edition(Pharmaceutical Press, 2012); Sundberg & Carey, Advanced OrganicChemistry: Parts A and B, 5th Edition (Springer, 2007).

Example 1: Preparation of Glycan Therapeutics

To a round bottom flask equipped with an overhead stirrer and a jacketedshort-path condenser was added one or more mono- or disaccharides alongwith 3-20% by dry weight of one or more of the catalysts described inU.S. Pat. No. 8,466,242 and WO 2014/031956, which are incorporatedherein by reference in their entirety. Water or another compatiblesolvent (1.54 equiv) was added to the dry mixture and the slurry wascombined at approximately 100 rpm using a paddle sized to match thecontours of the selected round bottom flask as closely as possible. Themixture was then heated to 80-155° C. Once the solids achieved a moltenstate, the vessel was placed under 10-1000 mbar vacuum pressure. Thereaction was stirred for 30 minutes to 8 hours, constantly removingwater from the reaction. Reaction progress was monitored by HPLC. Whensufficient oligomerization had occurred, the stirrer was shut off, thereaction was cooled to room temperature and vented to atmosphericpressure, and the solid mass was dissolved in a volume of watersufficient to create a solution of approximately 50 Brix (grams sugarper 100 g solution). Once dissolution was complete, solid catalyst wasremoved by filtration and the oligomer solution was concentrated toapproximately 50-75 Brix by rotary evaporation. In cases in which anorganic solvent has been used, water immiscible solvents can be removedby biphasic extraction and water miscible solvents can be removed byrotary evaporation concomitant to the concentration step.

Preparation of man100

To a 1000 mL round bottom flask equipped with an overhead stirrer and ajacketed short-path condenser was added 100 grams D-mannose along with7.14 g catalyst (5% by dry weight) and 50 mL water (50% by dry weight).The slurry was combined at approximately 100 rpm using a paddle sized tomatch the contours of the selected round bottom flask as closely aspossible. The mixture was then heated to 155° C. until the slurryachieved a molten state. The reaction was then placed under 300 mbarvacuum and stirred at 100 RPM for 3 hours, constantly removing waterfrom the reaction. After the pre-established time had elapsed, thestirrer was shut off, the reaction was vented to atmospheric pressure,and the slurry was cooled to room temperature. 100 mL of water (100% bydry weight) was added to the now solid mass and the material was allowedto dissolve over 16 hour to create a solution of approximately 50 Brix(grams sugar per 100 g solution). Once dissolution was complete, solidcatalyst was removed by filtration through a coarse glass-frittedfunnel. The catalyst was washed once with 25 mL water and the combinedliquids were carried on to the purification step.

Preparation of xyl100

To a 1000 mL round bottom flask equipped with an overhead stirrer and ajacketed short-path condenser was added 100 grams D-xylose along with7.11 g catalyst (5% by dry weight) and 50 mL water (50% by dry weight).The slurry was combined at approximately 100 rpm using a paddle sized tomatch the contours of the selected round bottom flask as closely aspossible. The mixture was then heated to 155° C. until the slurryachieved a molten state. The reaction was then placed under 300 mbarvacuum and stirred at 100 RPM for 2 hours, constantly removing waterfrom the reaction. After the pre-established time had elapsed, thestirrer was shut off, the reaction was vented to atmospheric pressure,and the slurry was cooled to room temperature. 100 mL of water (100% bydry weight) was added to the now solid mass and the material was allowedto dissolve over 16 hour to create a solution of approximately 50 Brix(grams sugar per 100 g solution). Once dissolution was complete, solidcatalyst was removed by filtration through a coarse glass-frittedfunnel. The catalyst was washed once with 25 mL water and the combinedliquids were carried on to the purification step.

Among others, the following 25 glycans were made in multiple batches andtested in various assays described herein:

Single glycan unit (homo-glycans): xyl100, rha100, ara100, gal100,glu100, and man100.

Two glycan units (hetero-glycans): ara50gal50, xyl75gal25, ara80xyl20,ara60xyl40, ara50xyl50, glu80man20, glu60man40, man60glu40, man80glu20,gal75xyl25, glu50gal50, man62glu38, and the hybrid glycans glu90sor10and glu90gly10.

Three glycan units (hetero-glycans): xyl75glu12gal12, xyl33glu33gal33,glu33gal33fuc33, man52glu29gal19, and glu33gal33neu33.

Example 2: Purification of Glycan Therapeutics

Oligosaccharides synthesized as in Example 1 were dissolved in deionizedwater to a final concentration of 25-50 Brix. The material was thenexposed to at least 2 mass equivalents of Dowex Monosphere 88 ionexchange resin. Exposure may occur by swirling in a flask at 120-170 rpmor by filtration through a wet slurry packed column as long as theresidence time is sufficient for the solution to achieve a final pHbetween 3 and 5. The oligomer solution was isolated by filtration (as inthe case of swirled reactions) or elution (as in the case of columnfiltration) and the process was repeated with Dowex Monosphere 77 ionexchange resin in an analogous fashion until the solution pH was above5.5. Finally the solution was exposed to Dowex Optipore SD-2 Adsorbentdecolorizing resin until the solution was sufficiently clarified andfiltered through a 0.2 micron filter to remove residual resin and resinfines. The final solution was then concentrated to 50-85 Brix by rotaryevaporation or to a solid by lyophilization.

Man100 and xyl100 were synthesized as in Example 1 and were purified byion exchange. The material was purified by elution through threedifferent ion-exchange chromatography columns using deionized water asan eluent at a speed of 2 bed volumes per hour. The columns werearranged serially in the following order: Dowex Monosphere 88 strongcation resin, Dowex Monosphere 77 weak base resin, and Dowex OptiporeSD-2 adsorbent decolorizing resin. Each column was 220 mL in bed volume.After passage, the solution was filtered through a 0.20 micron filter toremove residual resin and resin fines. The final solution was thenconcentrated to a 65-75 Brix syrup by rotary evaporation or to a 92-98Brix solid by lyophilization. Isolated yields of glycan varied bymonomeric content and preparation but were consistently between 80-85%by recovered mass and 88-94% by molar equivalent.

Example 3: Modification of Glycan Therapeutics by Removal of LowMolecular Weight Species

Oligomers prepared and purified as in Examples 1 and 2 were modified soas to remove low molecular weight species. The separation was achievedby osmotic separation. Approximately 45 cm of 1.0 kD MWCO Biotech CEdialysis tubing (31 mm flat width) from Spectrum Labs was placed intodeionized water and soaked for 10 minutes, then one end was sealed witha dialysis tubing clip. A 25 Brix solution of 8 grams dryoligosaccharide was sterile filtered and sealed into the tube with asecond clip along with a few mL of air to permit the tube to float. Thefilled tube was then placed in a 3 gallon tank of deionized water whichwas stirred with sufficient force to induce slow swirling of the sealedtubes. After 8 hours, the water in the tank was replaced and the tubewas allowed to stir for an additional 16 hours. Once the dialysis wascomplete and the material had a DP2+ yield greater than 95% and a DP3+yield greater than 90%, the dilute solution was sterile filtered andconcentrated in vacuo to a final concentration of approximately 65 Brixor lyophilized to a solid with a residual moisture between 1 and 10%.Alternatively, the separation was achieved by tangential flow filtration(TFF). In this case, 100 mL of 25 Brix glycan sample dissolved indeionized water and sterile filtered was placed into the feed bottle ofa Spectrum Labs KrosFlo Research IIi TFF system that was preparedaccording to the manufacturer's recommendation. The sample was thendiafiltered through a 1 kD mPES MidiKros hollow-fiber filter at atransmembrane pressure of 25 psig. HPLC samples of the feed stock takenevery 0.5 diafiltration volumes were used to determine when the materialhad a DP2+ yield greater than 95% and a DP3+ yield greater than 90% atwhich point the solution was sterile filtered and concentrated in vacuoto a 65 Brix syrup or lyophilized to a solid with residual water contentof 1-10% by mass. Low molecular weight oligomers can also be removed byprecipitation with 70% ethanol as in Gras, et al. Food Chem. 2001, 128,773-777. Glycans can also be fractionated into pools with differentaverage molecular weights by activated charcoal chromatography as inSanz, et al. Chromatographia 2006, 64, 233-236.

Example 4: Methods for Analyzing Preparations of Glycan Therapeutics

Measurement of Glycan Content by Liquid Refractometry

This experiment was designed to quantitate the amount of glycan in anygiven aqueous solution. A Mettler-Toledo Refracto 30GS portable sugarrefractometer was calibrated using high-purity reverse-osmosis deionizedwater. Several drops of the glycan solution were filtered through a 0.2micron syringe filter directly onto the lens of the refractometer. Themeasurement was taken at room temperature and reported as Brix. Theglycans were routinely concentrated to 75 Brix without obvioussolidification or crystallization at 23° C. Brix can then be convertedto solubility assuming a specific density of water equal to 1.0 g/mL.Thus, 75 Brix (100 grams of solution consisting of 75 grams of glycanand 25 grams of water) equals an aqueous solubility of 3.0 g/mL. As acomparison, the aqueous solubility of D-glucose is reported to be 0.909g/mL (48 Brix) at 25° C. by Sigma-Aldrich.

Monomeric Composition by Hydrolysis and GC-MS

This experiment was designed to quantitate the ratio of monomer contentwithin a given oligosaccharide. Glycosyl composition analysis wasperformed by combined gas chromatography/mass spectrometry (GC/MS) ofthe per-O-trimethylsilyl (TMS) derivatives of the monosaccharide methylglycosides produced from the sample by acidic methanolysis as describedpreviously by Santander et al. (2013) Microbiology 159:1471. Between 100and 200 □g of sample were lyophilized into a suitable test tube.Inositol (20 □g) was added to the sample as an internal standard, thenthe sample was heated to 80° C. in 1M HCl/methanol for 18 hours. Theresulting monosaccharides were then re-acetylated using pyridine andacetic anhydride in MeOH, and per-O-trimethylsilylated with Tri-Sil(Pierce) at 80° C. for 30 minutes. GC/MS analysis of the TMS methylglycosides was performed on an Agilent 7890A GC interfaced to a 5975CMSD, using a Supelco Equity-1 fused silica capillary column (30 m×0.25mm ID). Each peak was assigned to a component sugar based uponcomparison to known standards and integration of the respective peaksallowed clean calculation of the relative percentage of monomers withinan exemplified glycan. In all tested cases, the monomer composition of agiven oligosaccharide matched the input ratio within experimental errorand the output composition matched the input composition within theprecision of the measurement.

Molecular Weight Distribution by Size-Exclusion Chromatography (SEC)

This experiment was designed to quantitate the distribution of molecularweights within a given oligosaccharide. The measurement was made by HPLCusing the method described in Monograph of United States Pharmacopeia,38(6) In-Process Revision: Heparin Sodium (USP37-NF32). Separations wereachieved on an Agilent 1100 HPLC system via dual Shodex OHpak SB-802.5HQ columns using pure HPLC grade water as the eluent at 1.0 mL/min flowrate and an RI detector held at 40° C. The column temperature was set at40° C. and glucose (180 g/mol), maltose (342 g/mol), pullulan 1300 (1080g/mol; provided by Sigma-Aldrich), and pullulan 6000 (6100 g/mol;provided by Sigma-Aldrich) were used to draw a standard curve. A 1 mg/mLsolution of the sample was prepared and passed through a 0.22 μm syringefilter, followed by 10 μl injections into the HPLC. A third-orderpolynomial curve was constructed based on the logarithmic molecularweights and elution volumes of the listed standards. The weight-averagemolecular weight (Mw), the number average molecular weight (Mn), and thepolydispersity index (PDI) for the sample were calculated by comparisonto the standard curve. Table 5 contains the SEC data for man100 andxyl100.

TABLE 5 SEC measurements for glycan preparations of man100 and xyl100.Highest Mn Mw PDI observed MW glycan (g/mol) (g/mol) (Mw/Mn) (g/mol)Man100 371 1066 2.87   5941 Xyl100 417 1710 4.10 >10,000* *above thelimit of exclusion under these conditions

FIG. 1 shows the curve generated during the SEC evaluation of a glu100sample in which the average molecular weight was determined to be 1212g/mol or approximately DP7. The upper end of molecular weight of thematerial as defined by the point of the curve at 10% of maximumabsorption leading the curve was determined to be 4559 g/mol orapproximately DP28. The lower end of molecular weight of the material asdefined by 10% of the maximum absorption trailing the curve wasdetermined to be 200 g/mol or approximately DP1. Similar analysis of aglu50gal50 sample showed a MW, high mass, and low mass of 1195 g/mol(˜DP7), 4331 g/mol (˜DP27), and 221 g/mol (˜DP1) respectively.

Molecular Weight Distribution by Ion-Affinity Chromatography (IAC)

The proportion of glycan with DP greater than or equal to 2 (DP2+) and 3(DP3+) may be measured by ion-affinity chromatography. A sample ofglycan was diluted out to 50-100 mg/mL and 10 μL of this solution wasinjected onto an Agilent 1260 BioPure HPLC equipped with a 7.8×300 mmBioRad Aminex HPX-42A column and RI detector. Using pure HPLC-gradewater as an eluent, the sample was eluted at 0.6 mL/min through an 80°C. column and an RI detector maintained at 50° C. The peaks representingDP1-6 are assigned by comparison to reference standards and integratedusing the Agilent ChemStation software. Peaks are typically integratedas DP1, DP2, DP3, DP4-7, and DP8+. The DP that is achievable by thereaction described in Example 1 varies from monomer to monomer althoughit is consistent across batches if the procedure is followed correctly,e.g. glucose reliably achieves higher DP values than arabinose. Forexample, across 17 batches of glu100, DP2+ values ranged from 85-93% andDP3+ values ranged from 80-90%. Conversely, across 6 batches of ara100,DP2+ values ranged from 63-78% and DP3+ values ranged from 48-71%.Mixtures of monomers behaved as averages of the individual components.For man100 and xyl100 the DP2+ yield was 91.9% and 89.6, respectively,and the DP3+ yield was 85.5 and 85.5, respectively.

Alpha-/Beta-Distribution by 2D NMR

This experiment was designed to quantitate the ratio of alpha- andbeta-glycosidic bonds within a given sample by two-dimensional NMR.Approximately 150 mg of 65 Brix oligosaccharide solution was dried tostable mass in a vacuum oven at 45-95° C. under 400 mbar pressure. Thesample was subjected to two cycles of dissolution in D₂O and drying toremove residual H₂O. Once dried, the sample was dissolved in 750 μL D₂Owith 0.1% acetone, placed into a 3 mm NMR tube, and analyzed in a BrukerAvance-III operating at 500.13 MHz 1H (125.77 MHz 13C) equipped with aBruker BBFO probe operating at 21.1° C. The sample was analyzed using aheteroatomic single quantum coherence pulse sequence (HSQC) using thestandard Bruker pulse sequence. Anomeric protons between 4-6 ppm (1H)and 80-120 ppm (13C) were assigned by analogy to glucose as reported inRoslund, et al. (2008) Carbohydrate Res. 343:101-112. Spectra werereferenced to the internal acetone signal: 1H—2.22 ppm; 13C—30.8 ppm.Isomers were quantitated by integration of their respective peaks usingthe MNova software package from Mestrelab Research (Santiago deCompostela, Spain). FIG. 2 shows the anomeric region of a representativespectrum. Table 6 lists the distribution across 13 distinct combinationsof monomers showing the alpha-/beta-ratio to be as high as 4:1 as in thecase of rha100 and as low as 1:1 as in the case of glu50gal50.

TABLE 6 Distribution of alpha- and beta-bonds across batches and typesof glycans glycans alpha-bonds (%) beta-bonds (%) Glu100 58 42 61 39 6040 Gal100 60 40 Glu50gal50 50 50 56 44 Glu33gal33fuc33 55 45 Man100 5743 Man52glu29gal19 76 24 Ara100 67 33 Rha100 80 20 Xyl100 57 43 59 41Xyl75gal25 56 44Identification of Composition by NMR

This experiment was designed to identify the composition of a glycan by2D-NMR identification of the constituent monomers. Approximately 150 mgof 65 Brix oligosaccharide solution was dried to stable mass in a vacuumoven at 45° C. under 300 mbar pressure, typically requiring 4-8 hours.Once dried, the sample was dissolved in 1.0 mL D₂O with 0.1% acetone,placed into a 3 mm NMR tube, and analyzed in a Bruker Avance-III usingthe spectral parameters listed in Table 7. The sample was analyzed usinga 13C-1H heteroatomic single quantum coherence pulse sequence (HSQC)using the standard Bruker pulse sequence. Spectra were manually phasedthen referenced in both dimensions to the internal acetone signal:1H—2.22 ppm; 13C—30.89 ppm. The anomeric region of each glycan spectraderived from a single sugar monomer was then examined for peaksrepresenting specific glycosidic bonds characteristic to that monomer.Tables 7 and 8 list the diagnostic HSQC peaks for man100 and xyl100,respectively. FIGS. 7 a and 7 b show the HSQC spectra for man100 andxyl100, respectively.

TABLE 7 Spectral collection parameters used in HSQC fingerprintexperiments Parameter Value Solvent D2O Temperature 298.4 Pulse Sequencehsqcetgp Experiment HSQC Probe Z119470_0197 (PA BBO 500S1 BBF-H-D-05 ZSP) Number of Scans 8 Receiver Gain 123.5 Relaxation Delay 1.0000 PulseWidth 9.2000 Spectrometer Frequency (500.13, 125.77)  Spectral Width(3001.2, 13850.4) Lowest Frequency (778.0, 3213.4) Nucleus (1H, 13C)Acquired Size (1024, 512)  Spectral Size (1024, 1024) 

TABLE 8 Fingerprint peaks for man100 HSQC. F1: 13C (ppm) f2: 1H (ppm)110.2 5.15 109.8 5.22 109.2 5.28 108.0 5.09 105.7 5.24 102.9 5.13 102.85.03 102.0 5.24 101.8 5.10 101.8 5.39 101.4 4.98 101.1 4.70 100.1 4.90 99.2 4.77  97.9 5.22  97.7 4.83  95.8 5.12  94.6 5.16  94.3 4.88  93.15.37  92.6 5.29  85.3 4.82  85.1 4.76

TABLE 9 Fingerprint peaks for xyl100 HSQC f1: 13C (ppm) f2: 1H (ppm)108.8 5.06 107.1 5.12 104.3 5.21 104.0 4.66 103.9 4.44 103.6 5.20 103.24.55 102.6 5.28 102.4 4.46 101.6 5.16 100.6 5.11  99.5 5.31  99.2 4.91 99.0 4.76  98.0 5.36  97.2 4.56  92.7 5.18

Due to the spin-isolated nature of single carbohydrate rings withinpolysaccharides, the HSQC spectrum of a glycan with more than onemonomer is predicted to be represented by the sum of the HSQC peaks ofeach of its constituent sugars. Therefore, each constituent monomer hasunique HSQC peaks that will appear in any glycan that contains thatmonomer irrespective of other constituent monomers and furthermore, themonomers used to synthesize a glycan can be determined by identifyingthe fingerprint peaks unique to each constituent monomer. For example,FIG. 3 shows that the HSQC spectra of glu50gal50 is a hybrid of thespectra of glu100 and gal100. Table 10 lists the fingerprint peaks forselected glycan units.

TABLE 10 Diagnostic HSQC peaks for each component sugar. Monomer 1Hshift 13C shift Glucose 5.42 92.5 5.21 92.8 5.18 93.9 5.08 97.0 5.3698.4 5.34 99.8 5.38 100.3 4.95 98.6 4.62 96.6 4.70 103.6 4.49 103.4Galactose 5.37 92.9 5.24 93.1 5.14 96.0 4.96 99.3 5.31 98.7 5.39 101.45.00 101.8 4.80 101.3 4.63 97.0 4.56 97.2 4.53 103.1 4.43 104.1 Fucose5.18 92.9 5.33 92.4 5.04 96.3 4.90 99.7 4.52 97.0 4.39 103.6 Mannose5.37 93.0 5.16 94.6 4.88 94.2 5.39 101.7 5.24 101.9 5.13 102.8 5.03102.7 5.24 105.6 5.09 108.0 4.88 94.2 4.89 100.0 4.70 101.1 Xylose 5.1893.0 5.10 94.3 5.34 98.2 5.31 99.6 5.11 100.8 4.91 99.4 4.56 97.3 4.64104.2 4.54 103.4 4.44 104.1 Arabinose 5.22 93.2 5.13 93.2 5.29 96.0 5.2697.2 5.12 96.6 5.18 99.6 5.06 99.2 4.99 100.0 5.26 101.9 5.06 102.1 4.5597.4 4.54 105.2 4.50 105.5 4.38 103.9 Rhamnose 5.21 93.2 5.10 94.5 4.8594.1 5.01 95.8 5.35 100.5 5.15 102.2 5.04 102.9 4.78 97.9 4.71 99.0 4.72101.0

At least 5 peaks appeared for each glycan unit used as a startingmaterial in the synthesis of a glycan therapeutic containing 3 or fewerdistinct glycan units. The HSQC spectra of glycan therapeuticscontaining 4 or more distinct glycan units have at least 4 peaks foreach constituent glycan unit.

Branching Analysis

This experiment was designed to quantitate the distribution ofglycosidic regioisomers (branching) within a given oligosaccharide. Forglycosyl linkage analysis, the samples were permethylated,depolymerized, reduced, and acetylated; and the resultant partiallymethylated alditol acetates (PMAAs) analyzed by gas chromatography-massspectrometry (GC-MS) as described by Heiss et al (2009) Carbohydr. Res.344:915. The samples were suspended in 200 μl of dimethyl sulfoxide andleft to stir for 1 day. Permethylation was effected by two rounds oftreatment with sodium hydroxide (15 min) and methyl iodide (45 min). Theaqueous solution was hydrolyzed by addition of 2M trifluoroacetic acidand heating to 121° C. for 2 hours. Solids were isolated in vacuo andacetylated in acetic acid/trifluoroacetic acid. The resulting PMAAs wereanalyzed on an Agilent 7890A GC interfaced to a 5975C MSD (massselective detector, electron impact ionization mode); separation wasperformed on a 30 m Supelco SP-2331 bonded phase fused silica capillarycolumn. FIG. 4 shows three representative GC spectra from this analysis.These analyses show that the glycans had at least 0.1-10% of each of the1,2-; 1,3-; 1,4-, and 1,6-glycoside bond types. The materials alsocontained at least 5% of the branched bond types (including but notlimited to 1,3,6-; 1,4,6-; or 1,2,4-glycosides) and at least 3% of themonomeric units existed in the furanose form. A glycan originating froma single monomer consisted of at least 12 distinct non-terminalsubstitution patterns. A glycan originating from two monomers consistedof at least 18 distinct non-terminal substitution patterns. A glycanoriginating from three or more monomers consisted of at least 24distinct non-terminal substitution patterns.

Example 5: Effect of Glycans on Microbial Populations Ex Vivo

To determine the desired composition of glycans, bacterial cultures aregrown in the presence of candidate glycans and assayed for their growth,community composition (e.g., by 16S rRNA gene sequencing), production ofmetabolites, and phenotypic or transcriptomic properties. Desiredglycans are selected based on their ability to elicit desired propertieswithin the bacterial culture. Bacterial cultures include monocultures,mixed cultures, cultures isolated from humans or laboratory animalmodels, cultures isolated from a human or laboratory animal model andspiked with an isolate or collection of isolates, or cultures isolatedfrom a human or laboratory animal model and depleted of a collection ofspecies (for example, by application of an antibiotic). This assay canbe performed in the presence of antibiotics or other test compounds. Theresults obtained from the in vitro assays are compared with thoseobtained after treating humans with glycans or administering the glycansto a laboratory animal establishing the in vitro-in vivo correlation ofresults.

Example 6: Effect of Glycans on Commensal Bacteria In Vitro

An in vitro assay was performed to assess the ability of variousbacterial strains, including commensals of the gastrointestinal tract,to utilize different glycans as growth substrates. This assay wasdesigned to assess the ability of selected glycans to promote the growthof microbiota associated with effects on cancer progression, includingprotective effects. Bacterial strains were handled at all steps in ananaerobic chamber (AS-580, Anaerobe Systems) featuring a palladiumcatalyst. The chamber was initially made anaerobic by purging with ananaerobic gas mixture of 5% hydrogen, 5% carbon dioxide and 90% nitrogenand subsequently maintained in an anaerobic state using this sameanaerobic gas mixture. Anaerobicity of the chamber was confirmed dailyusing Oxoid anaerobic indicator strips that change color in the presenceof oxygen. All culture media, assay plates, other reagents and plasticconsumables were pre-reduced in the anaerobic chamber for 24-48 hoursprior to contact with bacteria. Glycans ara50gal50, glu33gal33fuc33,glu50gal50, gal100, glu100, xyl100, ara100, ara60xyl40, glu80man20,glu60man40, man52glu29gal19, man100, xyl75ara25, and a commerciallyavailable control, FOS (Nutraflora FOS; NOW Foods, Bloomingdale Ill.),were prepared at 5% w/v in water, filter-sterilized and added to Costar3370 assay plates for a final concentration of 0.5% w/v in the assay,with each glycan assayed in two non-adjacent wells and dextrose andwater supplied as positive and negative controls.

Bacterial isolates were obtained from the American Type CultureCollection (ATCC) and Leibniz Institute DSMZ-German Institute ofMicroorganisms and Cell Cultures (DSMZ). Cultures of the BacteroidetesBacteroides caccae ATCC 43185 “BCA.26”, Bacteroides thetaiotaomicronATCC 29741 “BTH.8”, Bacteroides cellulosilyticus DSM 14838 “BCE.71”,Parabacteroides distasonis ATCC 8503 “PDI.6”, Bacteroides vulgatus ATCC8482 “BVU.10” and Prevotella copri DSM 18205 “PCO.72”; the ClostridialesClostridium scindens ATCC 35704 “CSC.32”, Dorea formicigenerans ATCC27755 “DFO.36”, Dorea longicatena DSM 13814 “DLO.76”, Ruminococcus obeumATCC 29714 “ROB.74” and Blautia hansenii ATCC 27752 “BHA.20”; and theBifidobacteria Bifidobacterium longum ATCC 15707 “BLO.16” andBifidobacterium longum DSM 20088 “BLO.83”, were grown anaerobically inChopped Meat Glucose broth (CMG, Anaerobe Systems), a pre-reducedenriched medium including lean ground beef, enzymatic digest of casein,yeast extract, potassium phosphate, dextrose, cysteine, hemin andVitamin K1, for 18-48 hours at 37° C. Inocula were prepared bydetermining the optical density of each culture at 600 nM (OD₆₀₀) in aCostar 3370 polystyrene 96-well flat-bottom assay plate using a BiotekSynergy 2 plate reader with Gen5 2.0 All-In-One Microplate ReaderSoftware according to manufacturer's protocol, and diluting the cells toOD₆₀₀ 0.01 final in defined and semi-defined media that were preparedwithout sugars. B. vulgatus, D. formicigenerans, P. distasonis, B.longum, B. hansenii and D. longicatena isolates were tested in 900 mg/Lsodium chloride, 26 mg/L calcium chloride dihydrate, 20 mg/L magnesiumchloride hexahydrate, 10 mg/L manganese chloride tetrahydrate, 40 mg/Lammonium sulfate, 4 mg/L iron sulfate heptahydrate, 1 mg/L cobaltchloride hexahydrate, 300 mg/L potassium phosphate dibasic, 1.5 g/Lsodium phosphate dibasic, 5 g/L sodium bicarbonate, 0.125 mg/L biotin, 1mg/L pyridoxine, 1 m/L pantothenate, 75 mg/L histidine, 75 mg/L glycine,75 mg/L tryptophan, 150 mg/L arginine, 150 mg/L methionine, 150 mg/Lthreonine, 225 mg/L valine, 225 mg/L isoleucine, 300 mg/L leucine, 400mg/L cysteine, and 450 mg/L proline (Theriot C M et al. Nat Commun.2014; 5:3114), supplemented with 0-10% (v/v) CMG. B. thetaiotaomicron,B. caccae and B. cellulosyliticus were tested in 100 mM potassiumphosphate buffer (pH 7.2), 15 mM sodium chloride, 8.5 mM ammoniumsulfate, 4 mM L-cysteine, 1.9 μM hematin, 200 μM L-histidine, 100 μMmagnesium chloride, 1.4 μM iron sulfate heptahydrate, 50 μM calciumchloride, 1 μg/mL vitamin K3 and 5 ng/mL vitamin B12 (Martens E C et al.Cell Host & Microbe 2008; 4, 447-457). C. scindens, P. copri and R.obeum were tested in 10 g/L tryptone peptone, 5 g/L yeast extract, 0.5g/L L-cysteine hydrochloride, 0.1 M potassium phosphate buffer pH 7.2, 1μg/mL vitamin K3, 0.08% w/v calcium chloride, 0.4 μg/mL iron sulfateheptahydrate, 1 μg/mL resazurin, 1.2 μg/mL hematin, 0.2 mM histidine,0.05% Tween 80, 0.5% meat extract (Sigma), 1% trace mineral supplement(ATCC), 1% vitamin supplement (ATCC), 0.017% v/v acetic acid, 0.001% v/visovaleric acid, 0.2% v/v propionic acid and 0.2% v/v N-butyric acid(Romano K A et al. mBio 2015; 6(2):e02481-14). Bacteria were exposed toglycans ara50gal50, glu33gal33fuc33, glu50gal50, gal100, glu100, xyl100,ara100, ara60xyl40, glu80man20, glu60man40, man52glu29gal19, man100,xyl75ara25, commercial FOS and dextrose at a final concentration of 0.5%w/v in 96-well microplates, 200 μL final volume per well, at 37° C. for18-48 hours, anaerobically. OD₆₀₀ measurements for each isolate at theend of the incubation period were obtained using a Biotek Synergy2reader with Gen5 2.0 software according to manufacturer'sspecifications. Measurements were normalized by dividing the OD₆₀₀readings of the isolate on test glycans by the average OD₆₀₀ of theisolate in medium supplemented with 0.5% w/v dextrose to facilitatecomparison of glycan utilization by strains that grow withinsignificantly different OD₆₀₀ ranges. Table 11 provides a key to Tables12-14.

TABLE 11 Key Key to Glycans glycan # glycan identity  1 glu50gal50  2ara50gal50  3 glu100  4 gal100  5 glu80man20  6 glu60man40  7glu33gal33fuc33  8 ara100  9 man52glu29gal19 10 ara60xyl40 11 man80glu2012 xyl100 13 man100 14 xyl75ara25 15 FOS

Most glycans supported growth of most of the commensal strains tested inthe assay, with Average Normalized Growth values of at least 0.2.Glycans varied in the number and diversity of strains they supported(see Table 12) in the assay. In the assay, glu50gal50, ara50gal50,glu100, gal100, glu80man20, glu60man40, glu33gal33fuc33 and ara100supported growth of a combination of Bacteroidales; Clostridiales,including the Lachnospiraceae DFO.36, DLO.76, CSC.32 and BHA.20; andBifidobacteria. In the assay, man52glu29gal19, ara60xyl40 and man80glu20supported growth of a combination of Bacteroidales and Lachnospiraceae,and xyl100 and man100 supported growth of members of Bacteroidales.

TABLE 12 Glycan-supported growth of commensal bacteria. Commensals,Average Normalized Growth glycan # PDI.6 BVU.10 BTH.8 PCO.72 DFO.36DLO.76 CSC.32 BHA.20 BLO.16 BLO.83 1 ++ + + ++ ++ + + + − + 2 ++ ++ +++ + + + + − − 3 ++ + + ++ + + − + + − 4 + + + + ++ + + + − − 5 ++ + + +ND + + − + − 6 ++ + + − ND + + − + − 7 + + + − ++ + + − − − 8 − + +++ + + − − + − 9 ++ + + − + − + − − − 10 + + + + + − − − − − 11 ++ + + −ND ND + − − − 12 + + + + − − − − − − 13 ++ + + − ND − − − − − 14 − − − −− − − − − ND 15 ++ ++ + + + ++ + ++ ++ ++ Key symbol NGV − <0.2 +0.2-0.6 ++ >0.6 ND Not Determined

Glycans may increase the concentration of microbial proteins that aresufficiently similar to tumor antigens to elicit immune cell activityvia antigenic mimicry or cross-reactivity. Antigen mimicry may driveanti-tumor effects via two mechanisms. First, if microbes remainconfined in the intestinal lumen, microbes or microbial antigens arelocally captured by CD103+CD11b+ dendritic cells that migrate to thedraining lymph node to present relevant antigen to T cells.Subsequently, these T cells can traffic to the tumor to drive ananti-tumor immune response. A second mechanism is that microbialantigens, rather than T cells, can travel through the body to a tumorsite. Translocation of microbial proteins and even entire microorganismsfrom the intestine to mesenteric lymph nodes, the spleen, and othersites has been documented (Abt et al. (2012). Commensal bacteriacalibrate the activation threshold of innate antiviral immunity.Immunity 37, 158-170; Wheeler et al. (2014). The biology of bacterialpeptidoglycans and their impact on host immunity and physiology. Cell.Microbiol. 16, 1014-1023), and this breach of the mucosal barrier mayprove essential for instances in which antigenic mimicry determines thelong-range effects of the microbiome on immunosurveillance.Additionally, such antigenic mimicry may aid the immune systemsrecognition of pathogenic microorganisms that share antigens withmicrobial molecules that are exposed to the immune system.

In mouse models, the efficacy of such immune checkpoint blockade isstrongly dependent on the gut microbiome. CTLA4 blockade lost itstherapeutic activity against fibrosarcomas in mice that were eitherraised in a germ-free environment or that had been raised in specificpathogen-free conditions and then treated with multiple broad-spectrumantibiotics to sterilize the gut (Vetizou, et al. (2015). Anticancerimmunotherapy by CTLA-4 blockade relies on the gut microbiota. Science350, 1079-1084). This defect was overcome by gavage with Bacteroidesfragilis, by immunization with B. fragilis polysaccharides, or byadoptive transfer of B. fragilis-specific T cells, suggesting atherapy-relevant crossreactivity between microbial and tumor antigensrecognized by the same T cell receptor (TCR). Accordingly, both in miceand in patients, T cell responses specific for distinct Bacteroidesspecies (B. fragilis and B. thetaiotaomicron) were associated with theadministration (in humans) and efficacy (in mice) of CTLA-4 blockade.The microbiome also affects the therapeutic efficacy of PD-L1 blockade.Injection of a blocking antibody against PD-L1 was much more efficientin reducing the growth of melanomas in mice containing a high abundanceof Bifidobacterium in their gut than in mice lacking this genus.Bifidobacterium-treated mice exhibited significantly improved tumorcontrol compared with their untreated littermates, and this effect wasmediated by CD8+ T cells. DCs purified from mice that had been treatedwith Bifidobacterium were particularly active in presenting amelanoma-derived peptide antigen to T cells for stimulation of theirproliferation and IFN-g production, suggesting that Bifidobacteriumimproves the anticancer immune response through an effect on DCs (Sivanet al. (2015) Commensal Bifidobacterium promotes antitumor immunity andfacilitates anti-PD-L1 efficacy. Science 350, 1084-9), which mayincrease the presentation of a microbiome-derived antigen. By shiftingthe concentration of microbes present in the microbiome, the antigensmay also be shifted and the prevalence of antigens that mimictumor-associated antigens may be increased.

As shown in Table 13, most glycans supported growth of ParabacteroidesPDI.6 and Bacteroides isolates BVU.10, BTH.8, BCA.26 and/or BCE.71 withAverage Normalized Growth values of at least 0.2 in the assay. In theassay, glu80man20, glu100, glu60man40, glu50gal50 and ara100 supportedgrowth of Bifidobacterium longum, in addition to the BacteroidetesPDI.6, BVU.10, BTH.8, BCA.26 and/or BCE.71.

TABLE 13 Glycan-supported growth of Parabacteroides, Bacteroides andBifidobacteria Parabacteroides, Bacteroides and Bifidobacteria, AverageNormalized Growth glycan # PDI.6 BVU.10 BTH.8 BCA.26 BCE.71 BLO.16BLO.83 5 ++ + + ++ ++ + − 3 ++ + + ++ + + − 6 ++ + + + + + − 13++ + + + + − − 11 ++ + + + + − − 9 ++ + + + + − − 4 + + + ++ + − − 1++ + + + − − + 2 ++ ++ + ND ND − − 7 + + + + + − − 12 + + + − + − −10 + + + ND ND − − 8 − + + ND ND + − 14 − − − − − − ND 15 ++ ++ + ++ ++++ ++

As shown in Table 14, most glycans support the growth of at least onestrain of Clostridiales in the assay. The Clostridiales include theLachnospiraceae DFO.36, DLO.76, CSC.32 and BHA.20.

TABLE 14 Glycan-supported growth of Clostridiales Clostridiales, AverageNormalized Growth glycan # DFO.36 DLO.76 CSC.32 ROB.74 BHA.20  4++ + + + +  1 ++ + + − +  7 ++ + + + −  2 + + + ND +  5 ND + + + − 3 + + − − +  9 + − + + −  8 + + − ND −  6 ND + + − − 10 + − − ND − 11ND ND + − − 13 ND − − − − 14 − − − − − 12 − − − − − 15 + ++ + ++ ++

These data suggest that glycan therapeutics support growth of commensalbacteria.

Example 7: Collection of Fecal Samples

Fecal samples were collected by providing subjects with the FisherbrandCommode Specimen Collection System (Fisher Scientific) and associatedinstructions for use. Collected samples were stored with ice packs or at−80° C. until processing (McInnes & Cutting, Manual of Procedures forHuman Microbiome Project: Core Microbiome Sampling Protocol A, v12.0,2010, hmpdacc.org/doc/HMP_MOP_Version12_0_072910.pdf). Alternativecollection devices may also be used. For example, samples may becollected into the Globe Scientific Screw Cap Container with Spoon(Fisher Scientific) or the OMNIgene-GUT collection system (DNA Genotek,Inc.), which stabilizes microbial DNA for downstream nucleic acidextraction and analysis. Aliquots of fecal samples were stored at −20°C. and −80° C. following standard protocols known to one skilled in theart.

Example 8: Determining the Titer of Microbial Samples Collected fromFeces and Culturing Samples

To determine the titer of common bacteria of the gastrointestinal tract,fecal samples were collected as described in Example 7 and prepared as a10% weight/volume suspensions in sterile phosphate buffered saline(PBS). Ten-fold serial dilutions were prepared in sterile PBS and plated(100 μL per dilution) to Brucella Blood Agar (Anaerobe Systems;incubated anaerobically to non-selectively titer common member of thegut microbiota, including Bacteroides, or incubated aerobically tonon-selectively titer facultative anaerobes such as Proteobacteria).Bacteroides Bile Esculin Agar (Anaerobe Systems; cultured anaerobicallyto titer Bacteroides fragilis group), Cycloserine-Cefoxitin FructoseAgar (Anaerobe Systems; cultured anaerobically to titer Clostridiumdifficile), Lactobacillus-MRS Agar (Anaerobe Systems; culturedanaerobically to titer Lactobacillus), Eosin Methylene Blue Agar(Teknova; cultured aerobically to titer Escherichia coli and otherGram-negative enteric bacteria), Bile Esculin Agar (BD; culturedaerobically to titer Enterococcus species), Bifidobacterium SelectiveAgar (Anaerobe Systems; to titer Bifidobacterium species), or MacConkeyAgar (Fisher Scientific; to titer E. coli and other Gram-negativeenteric bacteria) may also be used. Plates were incubated at 37° C.under aerobic or anaerobic conditions as appropriate for the targetspecies. After 24-48 hours, colonies were counted and used toback-calculate the concentration of viable cells in the original sample.

To non-selectively culture samples containing bacteria collected from ahuman or laboratory animal model, rich media or agar such as BrucellaBlood Agar (Anaerobe Systems), Brain Heart Infusion Broth (Teknova), orChopped Meat Glucose Broth (Anaerobe Systems) were used. A minimal mediaformulation such as M9 (Life Technologies) supplemented with aminoacids, carbon sources, or other nutrients as needed were used tonon-selectively culture bacteria during in vitro assays testing theeffects of glycans or other compounds on bacterial populations.Alternatively, other minimal media formulations known to one skilled inthe art were used, for example, as reported in Martens et al. (MucosalGlycan Foraging Enhances Fitness and Transmission of a SaccharolyticHuman Gut Bacterial Symbiont, 2008, Cell Host & Microbe, 4:447-457).Alternatively, fecal slurries at a concentration of 0.1%-10%weight/volume in PBS were used in the presence or absence of additionalmedia elements for in vitro assays testing the effects of glycans orother compounds on bacterial populations.

Example 9: Effects of Glycans on Ex Vivo Human Fecal MicrobialCommunities

The ex vivo assay was designed to determine if glycans can modulate acomplex human fecal microbial community. Modulation of the community mayinduce functional and/or taxa shifts that may affect various hostresponses that may relate to the protection against or treatment ofdiseases, including cancer. Fecal samples and slurries were handled inan anaerobic chamber (AS-580, Anaerobe Systems) featuring a palladiumcatalyst. Glycans glu100, xyl100, man52glu29gal19, and a commerciallyavailable control, FOS (Nutraflora FOS; NOW Foods, Bloomingdale Ill.),were prepared at 5% w/v in water, filter-sterilized and added to 96-deepwell assay plates for a final concentration of 0.5% w/v, with eachglycan assayed in two non-adjacent wells and dextrose and water suppliedas positive and negative controls.

A human fecal sample donation was stored at −80° C. To prepare workingstocks the fecal sample was transferred into the anaerobic chamber andallowed to thaw. The fecal sample was prepared to 20% w/v in phosphatebuffered saline (PBS) pH 7.4 (P0261, Teknova Inc., Hollister, CA), 15%glycerol, centrifuged at 2,000×g, the supernatant was removed, and thepellet was suspended in PBS pH 7.4 to 1% w/v fecal slurry. Prepared 1%w/v fecal slurry were contacted with glycans to 500 μL final volume perwell, at 37° C. for 18 hours, anaerobically. Genomic DNA was extractedfrom the fecal samples and variable region 4 of the 16S rRNA gene wasamplified and sequenced (Earth Microbiome Projectprotocolwww.earthmicrobiome.org/emp-standard-protocols/16s/and CaporasoJ G et al. 2012. Ultra-high-throughput microbial community analysis onthe Illumina HiSeq and MiSeq platforms. ISME J.). Operational TaxonomicUnits (OTUs) were generated by aligning 16S rRNA sequences at 97%identity. Microbial communities were compared to each other usingUniFrac distance metric (Lozupone C. et al., Appl. Environ. Microbiol.December 2005 vol. 71 no. 12 8228-8235).

As shown in FIG. 8 a , Actinobacteria relative abundance is increasedwhile Bacteroidetes and Firmicutes relative abundance is decreased in 1%w/v fecal slurry in FOS control and glu100, compared to control fecalslurry lacking added carbon source. As shown in FIG. 8 b-e glu100 andFOS control significantly increased the relative abundance ofBifidobacteriales (FIG. 8 b ) and Bifidobacteria (FIG. 8 e ) compared tocontrol fecal slurry lacking added carbon source. Glu100 and FOS alsosignificantly reduced the relative abundance of Bacteroidales (FIG. 8 c) and Clostridiales (FIG. 8 d ). Xyl100 and man52glu29gal19 did not havea statistically significant effect in this assay. Modulation ofBifidobacterium and Bacteroides species is thought to play a role incontrolling and treating tumors (see Example 6).

Example 10: Effects of Glycans on Microbial Communities In Vivo inHealthy Human Volunteers

A Randomized, single-blind, cross-over, controlled study was conductedto analyze the effects of glycans on the microbiota of the human GItract. 45 healthy human volunteers were enrolled in the 35-day studywhich included a 7 day run-in period prior to randomization. Allvolunteers were between 18 and 40 years of age and had a BMI between 20and 27 kg/m². Following the 7 day run-in period, subjects that meteligibility criteria were randomized to one of three treatment groups of15 subjects each: glu50gal50, glu100 as a syrup, and a commercial FOScontrol in powder form. Subjects consumed the equivalent of 8 grams dryweight of glycan and FOS once a day for 7 days followed by a 7 daywashout period. They then consumed the equivalent of 16 grams dry weightof glycan and FOS once a day for 7 days followed by a 7 day washoutperiod. Subjects were instructed to mix the glycan and FOS with 200 mlof tap water prior to consumption.

The study identified two classes of taxa responding to glycan treatment(see, Table 15): (1) taxa that are in all or a large percentage ofindividuals, but respond robustly only in a subset of individuals (e.g.OTU 11 in individuals treated with glu50gal50) and (2) taxa that arefound in a small subset of individuals, but robustly respond in allsubjects (e.g. OTU 51 in glu100 and glu50gal50). Therapeutic glycansmodulated a larger number of OTU than the commercial FOS control: two inFOS and four each in glu100 and glu50gal50. The glycans showedoverlapping (OTU 11 and OTU 51) and differential modulation of OTUs(see, Table 15).

TABLE 15 OTUs that respond to glycan treatments in humans. Percentagesrepresent the approximate number of individuals in which the indicatedtaxa responded to the treatment. Percentages in the parenthesesrepresent the number of individuals Taxa FOS glu100 glu50gal50 OTU 11Blautia species 64% 29% (100%) (79%) OTU 10 Bifidobacterium 57% (93%)species OTU 2 Roseburia species 45% (93%) OTU 14 Coprococcus 64% (100%)species OTU 5 Lachnospiraceae 50% (family) (93%) OTU 50 Faecalibacterium36% (93%) prausnitzii OTU 20 Parabacteroides 62% (69%) species OTU 51Ruminococcaceae 43% 38% (38%) species (43%)

As can be seen from Table 15 not all subjects host all OTUs but OTUs 11,10, 2, 14, 5, 50, and 20 are present in most subjects tested (in about70% or more of subjects). For most OTUs growth modulation varies betweensubjects, some of which show modulation while others don't exhibit ashift in the taxa. For at least one OTU (OTU 51) all subjects hostingthe OTU showed a modulation. The microbial community in the subjects wasstable during the course of the study. Bacteria that were absent at thebeginning of the study did not appear during the course of the study(see FIG. 9 ). As shown in FIG. 9 for OTU 51, subjects that host the OTUshow growth of the OTU in the GI tract in response to the glycantreatment, often shortly after the begin of consumption of the glycan.Others that do not host the OTU do not show any changes in abundance forOTU upon administration of the glycan. Subjects may be classified asresponders and non-responders to glycans and may further be selected forglycan treatment, e.g. on the basis of the presence or absence ofparticular taxa.

Modulation of Bifidobacterium and Bacteroides species is thought to playa role in controlling and treating tumors (see Example 6). As shown inTable 16 the therapeutic glycan glu50gal50 modulated growth ofParabacteroides in 85% of the healthy human subjects in this study andFOS modulated Bifidobacterium in 57% of subjects.

TABLE 16 Genus that respond to glycan treatments in humans. Percentagesrepresent the approximate number of individuals in which the indicatedgenera responded to the treatment. Genus FOS glu50gal50 Bifidobacterium57% (100%) Parabacteroides 85% (100%)

These data suggest that the abundance of specific taxa, including taxapotentially involved in anti-cancer responses can be modulated in humansubjects by administering glycans.

Example 11: Effect of Glycans on Gene Expression in a Mouse Model

In a study two groups of mice are used. The control group of mice arefed with standard chow, and the different treatment groups of mice arefed with standard chow supplemented with glycans. After 1-30 days, bloodsamples are drawn from the mice, the mice are sacrificed, and tissuesfrom the intestine, liver, skin, and other sites of interest arecollected and stored at −80° C. RNA is isolated from the tissues andconverted to cDNA. The GeneChip Mouse Genome 430 2.0 Array (Affymetrix)is used to analyze the differential expression between the untreated andglycan-treated animals of approximately 14,000 murine genes. Theexperimental protocol and raw data analysis are performed according tothe manufacturer's instructions and standard protocols. The biologicalfunction of the differentially expressed genes and their involvement invarious processes are obtained from the following databases: RefGene(Reference for genes, proteins and antibodies: refgene.com/), CTD(Comparative Toxicogenomics Database: ctd.mdibl.org/), MGI (MouseGenomics Informatics: www.informatics.jax.org/), KEGG (KyotoEncyclopedia of Genes and Genomes: www.genome.jp/kegg/genes.html). Thisprocedure is used to identify the differential expression of genesencoding inflammatory cytokines, immunomodulatory cytokines,antimicrobial peptides, and other relevant effector molecules.

Example 12: Effect of Glycans on the Intestinal Microbiota of Naïve Mice

This study was carried out to assess the effect of glycan therapeuticson the gut microbiota of naïve mice. In this model, normal mice areadministered glycans in their drinking water over a period of 6 dayswith fecal samples taken from each mouse for 16S rRNA analysis.

Mice, C57Bl/6 (B6N Tac), mouse pathogen free (MPF; Taconic Biosciences,Germantown, NY) aged 8-10 weeks were housed singly in cages, with 6animals per dose group. Animals were fed PicoLab Rodent Diet 20 (“5053”;LabDiet, St. Louis, MO) or zero fiber diet (“ZFD”; Modified rodent dietAIN-93G: D15091701, Research Diets, New Brunswick, NJ) ad libitumthroughout the course of the study and had free access to water. Micewere maintained on a 12 h light/dark cycle. Mice were acclimated for 7days (days −7 to −1) prior to glycan administration.

Glycans were administered to the mice by inclusion in their drinkingwater at 1% weight/volume (w/v) from day 0 through day 5. Control micereceived water containing no glycan. Fresh fecal collections wereperformed for each mouse from days −2 to 5. Mouse weights were monitoredon days −1, 1, 3 and 4. Body weights of the mice did not changesignificantly throughout the course of the study.

Genomic DNA was extracted from the fecal samples and variable region 4of the 16S rRNA gene was amplified and sequenced (Earth MicrobiomeProject protocol www.earthmicrobiome.org/emp-standard-protocols/16s/ andCaporaso J G et al. 2012. Ultra-high-throughput microbial communityanalysis on the Illumina HiSeq and MiSeq platforms. ISME J.).Operational Taxonomic Units (OTUs) were generated by aligning 16S rRNAsequences at 97% identity. Microbial communities were compared to eachother using UniFrac distance metric (Lozupone C. et al., Appl. Environ.Microbiol. December 2005 vol. 71 no. 12 8228-8235).

Significant changes were observed when mice were administered a xyl 100preparation. UniFrac distances between microbiota sampled at one daybefore and 5 days after glycan administration were significantly largerin mice treated with xylose compared to mice who did not receive anyglycan (p=0.0043, Mann-Whitney test, FIG. 10 ). Alpha diversity wasmeasured by calculated Shannon Index in microbiota before and afterglycan or water administration. Shannon index significantly decreasedafter 5 days of xylose administration (p=0.0313, Wilcoxon paired test,FIG. 11 ).

The changes in observed shifts with administration of xylose wereattributed to an increase in relative abundance of sequences assigned togenus Akkermansia (phylum Verrucomicrobia, p=0.0313, Wilcoxon pairedtest, FIG. 12 a ), and genus Blautia (phylum Firmicutes, familyLachnospiraceae, p=0.0313, Wilcoxon paired test, FIG. 12 b ).

The most prominent Akkermansia species in the mammalian gut isAkkermansia muciniphila. Its preferred energy source is host intestinalmucin. Consumption of a low fiber diet and high intake of simple sugarsand fat results in decreased mucus production (British Journal ofNutrition/Volume 102/Issue 01/July 2009, pp 117-125, QuantitativeImaging of Gut Microbiota Spatial Organization, Earle K A et al, CellHost Microbe. 2015 Oct. 14; 18(4):478-88). Thinning of intestinal mucusmay result in increased gut permeability and translocation ofmicroorganisms or their components, such as lipopolysaccharide (LPS),which induce inflammation. LPS levels are increased upon consumption ofhigh fat diet in rodents which then develop metabolic syndrome(Metabolic endotoxemia initiates obesity and insulin resistance, Cani PD et al, Diabetes. 2007 July; 56(7):1761-72).

Bacteroidetes, may induce the growth of Akkermansia. For example,colonization of germ free mice with Bacteroides thetaiotaomicron inducesmucus production by intestinal goblet cells (Wrzosek et al. BMC Biology2013 11:). This may create a favorable environment for Akkermansiagrowth. Consumption of mucus by Akkermansia may stimulate increasedmucus production and play a role in the restoration of the gut barrierthat prevents leaking of microbial endotoxin LPS. Decreased endotoxemiareduces inflammation. Inflammation precedes most cancers. Bronchitis,colitis, cervicitis, gastritis, and hepatitis, for example, reflectinflammation of the bronchus, colon, cervix, stomach, and liver,respectively. Many cancers, especially solid tumors, appear to bepreceded by inflammation of a given organ. For instance, people whosmoke cigarette develop bronchitis, and 15% to 20% of these peopledevelop lung cancer (Wingo et al. Annual report to the nation on thestatus of cancer, 1973-1996, with a special section on lung cancer andtobacco smoking. J Natl Cancer Inst 1999; 91:675-90). Similarly, peoplewho have colitis are at high risk of developing colon cancer (Itzkowitz,Inflammation and cancer IV. Colorectal cancer in inflammatory boweldisease: the role of inflammation. Am J Physiol Gastrointest LiverPhysiol 2004; 287:G7-1734). Infection with Helicobacter pylori caninduce gastritis, which in its chronic form can lead to gastric cancer(Peter, Helicobacter pylori and gastric cancer: the causal relationship.Digestion 2007; 75:25-35).

Akkermansia muciniphila metabolites include the SCFA propionate which isalso thought to modulate inflammation (see, Example 15). Glycantherapeutics when administered in an effective amount may modulatebacterial species, such as, e.g., Akkermansia that play a role in thereduction of inflammation.

Example 13: Effect of Glycans on the Colonic Epithelium of MiceChallenged with an Inflammatory Agent

This study was carried out to assess the effect of glycan therapeuticson the host gene expression in the large intestine. Glycan treatment mayalter inflammatory pathways in the gastrointestinal tract and decreaseinflammation in the gastrointestinal tract, which may prevent thedevelopment of cancer.

In this model, normal mice were administered glycans (non-fermentableAcacia fiber, Glu100 or Man52glu29gal19) in their drinking water over aperiod of 21 days. On days 8-13 all mice were treated with 2.5% Dextransulfate sodium (DSS) to induce intestinal inflammation. Dextran sulfatesodium is a chemical that drives inflammation in the intestine ofanimals. On day 21 mice were sacrificed by CO₂ asphyxiation. Two 3-5 mmadjacent sections of flushed colon were placed in 2 separate freezervials and snap frozen. Messenger RNA was extracted and sequenced onIllumina HiSeq sequencer.

Animals treated with non-fermentable Acacia fiber, lost significantlymore weight and had higher endoscopy score than those who receivedeither Glu100 or Man52glu29gal19 (p<0.05, Kruskal-Wallis test withDunn's multiple comparisons), suggesting that the glycans reducedinflammation in the animals.

Sequences from each animal were mapped to mouse genome and number ofsequences mapped to each gene were quantified using htseq-count software(HTSeq—a Python framework to work with high-throughput sequencing data.Anders S, Pyl P T, Huber W. Bioinformatics. 2015 Jan. 15; 31(2):166-9.doi: 10.1093/bioinformatics/btu638. Epub 2014 Sep. 25). Genesdifferentially expressed between groups were determined using DeSeq2package in R (Michael I Love, Wolfgang Huber, Simon Anders: Moderatedestimation of fold change and dispersion for RNA-seq data with DESeq2.Genome Biology 2014, 15:550).

There were 182 genes differentially expressed (p value adjusted formultiple comparison <0.05) between animals treated with Glu100 andcontrol animals who did not receive any treatment. Of those, 92 geneswere also differentially expressed between animals treated withMan52glu29gal19 compared to control animals. The latter comparisonrevealed additional 531 genes that were significantly different in theirexpression between 2 groups. A majority of genes that weredown-regulated in mouse host treated with glycans are involved ininflammatory responses: complement pathway, apoptosis, antigenpresentation, oxidative stress, cell adhesion and cytoskeletonremodeling. The data suggest that altered genetic regulation in responseto glycan treatment decreased the inflammation which can be a requisitefor the development of cancer.

Genes that were upregulated in mice treated with glycans were involvedin Notch signaling and Wnt signaling pathways, which control cellproliferation, migration and tissue regeneration. This could be a signof more active epithelial regeneration induced by functional shifts ofthe microbiota as a result of the glycan treatment.

Example 14: In Vitro Co-Culture Models to Test the Effect of Glycans onHost Responses to Bacterial Communities at Intestinal Sites

Bacteria can elicit both pro- and anti-inflammatory responses from host(mammalian) cells, and different bacterial species can elicit differenthost responses. The immune system and pro- and anti-inflammatoryresponses are linked to diseases, disorders or pathological conditionsrelated to, e.g., immune imbalances, nutritional imbalances which canlead to and may be associated with cancers. Preparations of glycans areused to alter the bacterial population to elicit a desired hostresponse. An in vitro co-culture model is used to measure the hostresponses elicited by bacterial populations grown in the presence ofglycans. Glycans that promote bacterial populations that elicitbeneficial host responses or minimize detrimental host responses areselected using this assay.

Epithelial cell lines or tissues from the intestine are used in aco-culture model (Haller D, Bode C, Hammes W P, Pfeifer A M A, SchiffrinE J, Blum S, 2000. Non-pathogenic bacteria elicit a differentialcytokine response by intestinal epithelial cell/leucocyte co-cultures.Gut. 47:79-97) (Borruel et al., 2003. Effects of nonpathogenic bacteriaon cytokine secretion by human intestinal mucosa. Am J Gastroenterology.98:865-870). Human enterocyte-like CaCO-2 cells are seeded at a densityof 2.5×10⁵ cells/ml on 25 mm cell culture inserts (0.4 μm nucleoporesize; Becton Dickinson). The inserts are placed into 6-well tissueculture plates (Nunc) and cultured 18-22 days at 37° C./10% CO₂ in DMEM(glutamine, high glucose; Amimed) supplemented with 20% heat-inactivatedfetal calf serum (56° C., 30 minutes; Amimed), 1% MEM non-essentialamino acids (Gibco BRL), 10 μg/ml gentamycin (Gibco BRL), and 0.1%penicillin/streptomycin (10 000 IU/ml/10 000 UG/ml; Gibco BRL). The cellculture medium is changed every second day until the cells are fullydifferentiated. Alternatively, a 3D reconstructed tissue model producedfrom normal, human cell-derived small intestine epithelial andendothelial cells and fibrobasts (Epilntestinal model; MatTekCorporation, Ashland, MA) is used. Transepithelial electrical resistance(TEER) is determined using a MultiCell-ERS voltmeter/ohmmeter. Tissueculture inserts are washed twice with prewarmed antibiotic-free mediumprior to challenge with bacterial cultures. Separately, bacterialcultures are grown in the presence of preparations of glycan. After16-24 hours of growth in the presence of glycans, the bacterialsuspensions are prepared in antibiotic-free medium and 10⁶-10⁸ CFU areadded to confluent cell or tissue cultures. The co-cultures areincubated at 37° C. for 4-24 hours.

At the conclusion of the co-incubation period, the supernatant iscollected and analyzed for inflammatory and immunomodulatory cytokinesincluding IL-1α, IL-1β, TNF, IL-8, RANTES, IL-10, TGF-β, IFN-γ, IL-4,IL-6, IL-12, IL-17, and IL-23. This analysis is performed by enzymelinked immunosorbent assay (ELISA) or other comparable quantificationtechnique (e.g., Luminex Assay; Life Technologies, Carlsbad, CA)following standard protocols. To analyze a broader range of responses,gene expression (e.g., by microarray) or transcriptomic (e.g., byRNA-Seq) analysis is performed by lysing the cells, purifying RNA, andfollowing standard protocols. This procedure is used to analyze theexpression of genes encoding inflammatory cytokines, immunomodulatorycytokines, antimicrobial peptides, and other relevant host responses.

Example 15: Effect of Glycans on Microbial SCFA Metabolite Production InVitro

An in vitro assay was performed to assess the production of short chainfatty acids by gut commensal bacteria cultured with the glycanglu80man20 or commercially available FOS as a carbon source. Strainswere handled under strictly anaerobic conditions in an AS-580 anaerobicchamber (Anaerobe Systems) using pre-reduced reagents and materials. TheBacteroidete Bacteroides uniformis (ATCC 8492) “BUN.80” was tested in100 mM potassium phosphate buffer (pH 7.2), 15 mM sodium chloride, 8.5mM ammonium sulfate, 4 mM L-cysteine, 1.9 μM hematin, 200 μML-histidine, 100 μM magnesium chloride, 1.4 μM iron sulfateheptahydrate, 50 μM calcium chloride, 1 μg/mL vitamin K3 and 5 ng/mLvitamin B12 (Martens E C et al. Cell Host & Microbe 2008; 4, 447-457).The Lachnospiracea Dorea longicatena (DSM 13814) “DLO.76” was tested in900 mg/L sodium chloride, 26 mg/L calcium chloride dihydrate, 20 mg/Lmagnesium chloride hexahydrate, 10 mg/L manganese chloride tetrahydrate,40 mg/L ammonium sulfate, 4 mg/L iron sulfate heptahydrate, 1 mg/Lcobalt chloride hexahydrate, 300 mg/L potassium phosphate dibasic, 1.5g/L sodium phosphate dibasic, 5 g/L sodium bicarbonate, 0.125 mg/Lbiotin, 1 mg/L pyridoxine, 1 m/L pantothenate, 75 mg/L histidine, 75mg/L glycine, 75 mg/L tryptophan, 150 mg/L arginine, 150 mg/Lmethionine, 150 mg/L threonine, 225 mg/L valine, 225 mg/L isoleucine,300 mg/L leucine, 400 mg/L cysteine, and 450 mg/L proline (Theriot C Met al. Nat Commun. 2014; 5:3114), supplemented with 10% (v/v) ChoppedMeat Glucose broth (Anaerobe Systems). Bacteria were exposed to eitherglycan glu80man20 or FOS at 0.5% (w/v) final and incubated at 37° C. for39-50 hours. Following incubation, cells were pelleted from 1.5 mLaliquots of cultures in duplicate by centrifugation at 18,000×g for fiveminutes, the supernatant was sterilized through a 0.22 umpolyethersulfone filter, and the supernatant was stored at −80° C. or ondry ice until it was analyzed. Short chain fatty acid (SCFA) analysiswas performed on the filtered culture supernatants using a coldextraction of short chain fatty acids, measured by EI-CGMS withoutderivatization. FIG. 13 summarizes the results obtained. In the assay,cultures of Bacteroidete BUN.80 and Lachnospiracea DLO.76 grown witheither glycan glu80man20 or FOS produced supernatants with total SCFAconcentrations in excess of 5,000 μM. Acetate was the SCFA produced inthe highest concentrations in the assay, and propionate was produced atthe second-highest levels. Butyrate, isovalerate, valerate, hexanoateand octanoate were also detected in the assay.

Example 16: Effect of Glycans on Microbial SCFA Metabolite Production InVivo

To assess the production of short chain fatty acids by gut commensalbacteria upon glycan administration in vivo, short chain fatty acidanalysis was performed on 30-50 mg of cecal contents from mice fedeither a High Fat diet (Research Diets D12492), Normal Mouse chow(Research Diets D12450), or High Fat diet+glycan using a GC-basedmethod. High fat diets are associated with pro-inflammatory states andthe development of colonic cancers. Treatment with glycans (glu100 at 6%or man52glu29gal19 at 1%) reduced the abundance of both butyrate andpropionate in the cecal contents of mice compared to high fat diet alone(FIG. 14 ). As shown in Table 17, glycans reduced the levels of certainSCFAs in this study.

TABLE 17 Glycans reduce SCFAs. (− indiciates P < 0.05, Wilcox, FDRcorrected) glu100 man52glu29gal19 Acetate Propionate − − Butyrate − −Isovalerate − − Valerate − − Hexanoate − − Heptanoate − − Octanoate − −

The decrease in short chain fatty acids due to glycan treatment (FIG. 14and Table 17) may increase the propensity of T cells that differentiatein the gastrointestinal tract to become inflammatory T cells (e.g. Th17)that can traffic to tumor sites and drive inflammatory responses againstthe tumor. SCFAs constitute an important energy source for colonocytesand also function as signaling molecules, modulating intestinalinflammation, and metabolism. SCFAs, in particular acetate, propionate,and butyrate, favor histone H3K27 acetylation and increased expressionof the Treg-specific transcription factor gene, Foxp3, thereby boostingTreg development in the gastrointestinal tract (Furusawa et al., 2013.Commensal microbe-derived butyrate induces the differentiation ofcolonic regulatory T cells. Nature 504, 446-450). These Tregs are absentin germfree mice that lack both commensal bacteria and theirmetabolites, such as the short-chain fatty acid (SCFA) butyrate, and arenecessary for their development (Arpaia et al., 2013 Metabolitesproduced by commensal bacteria promote peripheral regulatory T-cellgeneration. Nature 504, 451-455; Atarashi et al., 2011 Induction ofcolonic regulatory T cells by indigenous Clostridium species. Science331, 337-341; Furusawa et al., 2013). The modulation of T cell functionby the microbiota, through SCFAs, toward tolerance (IL-10 secretion)rather than inflammation (IL-17 secretion) has also been proposed forIL-10/IL-17 double-secreting T cells. Thus, T cells can switch from atolerance to inflammatory phenotype and vice versa based on the presenceor absence of SCFAs (Ruff and Kriegel, 2015, Autoimmune host-microbiotainteraction at barrier sites and beyond. Trends Mol. Med. 21, 233-244),and the decrease of SCFAs driven by glycans likely leads to an increasein inflammatory T cells. It is also well-appreciated in the art thatTh17 cells primed in the intestine could traffic to peripheral sites,undergo functional plasticity, and mediate inflammation: A number ofmouse models of chronic inflammation residing in distant, non-mucosaltissues, where an impact of the gut microbiota was demonstrated,outlined the pro-inflammatory role of intestinal Th17 cells (Lee et al.,2011, Proinflammatory T-cell responses to gut microbiota promoteexperimental autoimmune encephalomyelitis. Proc. Natl. Acad. Sci. USA108 (Suppl 1), 4615-4622; Wu et al., 2010, Gut-residing segmentedfilamentous bacteria drive autoimmune arthritis via T helper 17 cells.Immunity 32, 815-827; Yang et al., 2014, Focused specificity ofintestinal TH17 cells towards commensal bacterial antigens. Nature 510,152-156). It has been shown in the art that an increase in inflammatoryT cells or increase in activity of inflammatory T cells in a tumor candrive improved control over cancer (Sharma and Alison, 2015, Immunecheckpoint targeting in cancer therapy: toward combination strategieswith curative potential. Cell 161, 205-214).). The decreased generationof tolerogenic T cells may also lead to an activation of inflammatoryfunctions against pathogens or infections resulting from decreasedinflammatory immune function. Both pro- and anti-inflammatory responsesare linked to diseases, disorders or pathological conditions related to,e.g., immune imbalances, nutritional imbalances and cancers.

Example 17: Effect of Glycans on Total Microbial Metabolite ProductionIn Vivo

Untargeted metabolomics was performed on 30-50 mg of cecal contents frommice fed either a High Fat diet (Research Diets D12492), Normal Mousechow (Research Diets D12450), or High Fat diet+glycan using Metabolon'sLC-MS based DiscoveryHD4 platform. A total of 538 metabolites wereidentified and 149 were differentially abundant in High Fat vs. NormalChow, 26 with treatment with glu100 0.3%, and 36 with treatment withman52glu29gal19 1% (Tables 18 and 19). Treatment with glycanssignificantly shifted the composition of the mouse cecal metabolome(P<0.01, adonis, FIG. 15 ).

TABLE 18 Total differentially abundant metabolites between diets andwith glycan treatments. P < 0.05, Welch's T-test. High Fat High Fat vs.High Fat vs. vs. High Fat + High Fat + Normal glu100 man52glu29gal19Chow 0.3% 1% Number of metabolites 149 26 36 significantly different (p< 0.05) INCREASE  81 19 19 DECREASE  68  7 17

TABLE 19 Differentially abundance metabolites between High Fat dietcontrol vs. High Fat diet with the addition of glycan treatment. P <0.05, Welch's T-test. SUPER PATHWAY SUB PATHWAY BIOCHEMICAL Amino AcidAlanine and Aspartate N-acetylasparagine MetabolismN-acetylaspartate.(NAA) Creatine Metabolism guanidinoacetate GlutamateMetabolism N-acetylglutamine Methionine, Cysteine, cysteine SAM andTaurine cysteine.sulfinic.acid Metabolism N- acetylmethionine.sulfoxidePhenylalanine and N-formylphenylalanine Tyrosine Metabolismphenol.sulfate Polyamine Metabolism N1,N12-diacetylspermine TryptophanMetabolism indoleacetate kynurenate Carbohydrate Aminosugar Metabolismdiacetylchitobiose Disaccharides and sucrose Oligosaccharidesgalactonate Fructose, Mannose and mannitol/sorbitol Galactose Metabolismmannose Glycolysis, glucose Gluconeogenesis, and Pyruvate MetabolismPentose Metabolism xylose Cofactors and Pantothenate and CoA pantethineVitamins Metabolism Lipid Carnitine Metabolism carnitine Fatty AcidSynthesis malonate Fatty Acid, Dicarboxylate octadecanedioate.(C18)Fatty Acid, 2-hydroxypalmitate Monohydroxy Long Chain Fatty Acidpentadecanoate.(15:0) Lysolipid 1-oleoyl-GPG.(18:1)*1-palmitoyl-GPE.(16:0) Primary Bile Acid cholate Metabolismtauro-beta-muricholate Secondary Bile Acid taurodeoxycholate Metabolismtaurohyodeoxycholic.acid taurolithocholate tauroursodeoxycholateursodeoxycholate Sphingolipid Metabolism 3-ketosphinganine NucleotidePurine Metabolism, inosine (Hypo)Xanthine/Inosine containing PurineMetabolism, guanosine Guanine containing Pyrimidine Metabolism, uridineUracil containing Peptide Dipeptide valylleucine Unknown UnknownX.-.12101 X.-.14254 X.-.14302 X.-.15806 X.-.15843 X.-.17438 X.-.17852X.-.21365 X.-.21788 X.-.22035 X.-.22062 X.-.24664 X.-.24670 X.-.24721X.-.24831 Xenobiotics Food Component/Plant enterolactone stachydrine

The data suggest that glycan treatment modulates the total metaboliteoutput of the GI tract microbiota in the animal including SCFAs (seeExample 16) and bile acids (see Example 18). Metabolic changes andpotential links to the immune system and inflammatory responses arethought to play a role in diseases, disorders or pathological conditionsrelated to, e.g., immune imbalances, nutritional imbalances and cancers.

Example 18: Effect of Glycans on Bile Acid Production In Vivo

The production of certain bile acids, such as deoxycholic acid (DOC) andLithocholic acid (LCA) which are associated with a high fat diet havebeen linked to cancer development. Deoxycholic acid (DOC) is secondarybile acid produced solely by the 7a-dehydroxylation of primary bileacids carried out by anaerobic gut bacteria from the genus Clostridium.DOC can be considered as a microbial co-carcinogen that not onlycontributes to colon carcinogenesis, but that also participates to thedevelopment of liver cancer, presumably by inducing thesenescence-associated secretory phenotype of hepatic stellate cells,thereby stimulating pro-inflammatory and tumor-promoting reactions in amouse model of obesity-associated hepatocellular carcinoma (Yoshimoto etal., 2013, Obesity-induced gut microbial metabolite promotes livercancer through senescence secretome. Nature 499, 97-101). DOC may wellcooperate with other bacterial products, including LPS, in promotinghepatocellular carcinoma (Dapito et al., 2012, Promotion ofhepatocellular carcinoma by the intestinal microbiota and TLR4. CancerCell 21, 504-516). Numerous other studies have shown that DOC inducesapoptosis in colon cells in short-term cultures.

Bile acid analysis was performed on 30-50 mg of cecal contents from micefed either a High Fat diet (Research Diets D12492), Normal Mouse chow(Research Diets D12450), or High Fat diet+glycan using Biocrates LC-MSbased Bile Acid Kit. Glycan treatment significantly altered the bileacid composition of the mouse cecum (FIG. 16 , Table 20), while totalbile acid pool size did not change.

TABLE 20 Bile acid species that are significantly different with glycantreatment (P < 0.05, Wilcoxon Rank Sum with FDR correction for multiplehypotheses) Bile Acid Type Glycodeoxycholic acid SecondaryGlycolithocholic acid Secondary Alpha-Muricholic acid PrimaryBeta-Muricholic acid Primary Taurocholic acid PrimaryTaurochenodeoxycholic acid Primary

As shown in FIG. 17 , glycan treatment resulted in a reduction of (A)DCA (deoxycholic acid) and (B) LCA (lithocholic acid) compared to highfat control. The reduction in bile acids resulting from glycan treatmentmay prevent the development of cancer.

Many undiscovered links between other bile acids and the development ofcancer may exist. For example, the concentration of Glycodeoxycholicacid, Glycolithocholic acid, Alpha-Muricholic acid, Beta-Muricholicacid, Taurocholic acid, and Taurochenodeoxycholic acid, which are allsignificantly altered by glycan treatment (Table 20) may affect cancerdevelopment. Furthermore, population-based studies have shown thatsubjects who consume high-fat and high-beef foods display elevatedlevels of fecal secondary BAs, mostly DOC and LCA, as do patientsdiagnosed with colonic carcinomas. Glycan treatment may modulate thebile acids present in the gastrointestinal tract of subjects consuming ahigh fat diet to prevent cancer development. Furthermore, the decreasein inflammation resulting from alterations of bile acids maysystemically decrease inflammatory cell numbers across the body andthereby may influence diseases that are related to aberrant immuneinflammatory activation, e.g., auto-immune diseases and other diseasesrelated to eimmune imbalances and nutritional imbalances.

Example 19: Effect of Glycans on Chemotherapy-Induced Toxicity andImmune Responses In Vivo

This study was conducted to elucidate the effects of glycan therapeuticson chemotherapy-induced toxicity in a modified rat model (Fukudome etal., Diamine oxidase as a marker of intestinal mucosal injury and theeffect of soluble dietary fiber on gastrointestinal tract toxicity afterintravenous 5-fluorouracil treatment in rats, Med Mol Morphol. 2014June; 47(2):100-7). Off-target toxicity of chemotherapeutics includingdiarrhea, oral and gastrointestinal mucositis, and leukopenia andneutropenia, can limit dose and frequency of treatment, and can causesignificant suffering and decreased quality of life in affectedpatients. In these studies, normal rats were treated with glycans andthe chemotherapeutic drug 5-fluorouracil (5-FU), then monitored formanifestations of toxicity including weight loss, diarrhea, andhematological effects.

In this study, 75 male Sprague-Dawley rats (Charles River Laboratories)were randomized into five groups of fifteen animals each, and eachanimal was individually housed. The rats were allowed to acclimate forfour days following arrival, and starting on Day −7, animals in fourglycan-treated groups began treatment with novel glycan compositions(glu100, glu50/gal50, glu33/gal33/fuc33, or man100) at 2.5% wt/wt adlibitum in drinking water; treatment with glycans continued through Day9. During this same period, animals in the control group received plainwater. Beginning on Day 0, all rats were dosed with 5-FU (100 mg/kg in0.2 mL/100 g) via intraperitoneal injection once daily through Day 3.Daily, rats were weighed, monitored for survival, and assessed visuallyfor the presence of diarrhea. Animals exhibiting weight loss greaterthan 30% were euthanized. Diarrhea severity was scored on a scale of 0-4as follows: a score of 0 indicates a normal, well-formed pellet; a scoreof 1 indicates a loose stool that is soft but stays in shape; a score of2 indicates a loose stool of abnormal form with excess moisture; a scoreof 3 indicates watery stool or diarrhea; and a score of 4 indicatesbloody diarrhea. On Day 5, non-terminal blood samples were collected viaretro-orbital bleed from 7-10 rats/group and a complete blood count wasperformed.

While there were no significant differences in body weight or diarrheascore between control and glycan-treated rats in this study,administration of glu/gal/fuc significantly increased white blood cellcount on Day 5 (p<0.05) compared to 5-FU treatment alone (FIG. 18 ).

Treatment with 5-FU elicits a number of off-target toxicities, includingneutropenia and leukopenia. In this study, treatment of rats withglu/gal/fuc increased the white blood cell count compared to 5-FUtreatment alone. In an inflammatory response, white blood cells(leukocytes, neutrophils, macrophages, or monocytes) are recruited tothe site of injury in response to damage, e.g. to the intestinal mucosa,caused by the 5-FU insult. A potential mechanism for the increase inWBCs by glu/gal/fuc may be through direct or indirect action upon theproduction of short chain fatty acids (SCFAs) via the gut microbiota.Bacterially-derived SCFAs have demonstrated both pro- andanti-inflammatory actions, depending upon the cell type affected; SCFAsmay inhibit leukocyte function and migration, but may also increaseaccumulation of neutrophils (Vinolo et al., Regulation of inflammationby short chain fatty acids, Nutrients. 2011 October; 3(10)). Whilefurther analysis is required to determine the subpopulation(s) of whiteblood cells affected by glu/gal/fuc, the increase in WBCs seen withglu/gal/fuc may confer an increased ability to react to bacterialinfiltration across the gut membrane and thus ameliorate some of thetoxic effects of 5-FU treatment. In this way, glu/gal/fuc or similarglycans may decrease the presentation or severity of side effects andpossibly prevent the need to decrease 5-FU dose or frequency. Severaldrug toxicities are also related to or associated with immune imbalancesand nutritional imbalances apart from cancer.

Example 20: Effect of Glycans on Drug Toxicity and GI Tract Motility InVivo

This study was conducted to analyze the effects of glycan therapeuticsin a mouse model of opioid-induced constipation. In this model, normalmice are dosed with glycan or control for several days and thenadministered a dose of morphine sufficient to produce decreasedgastrointestinal (GI) transit and colonic propulsion (Coates et al. 2006Neurogastroenterol Motil 18:464-471). In humans, morphine and relatedopiate drugs are known to cause constipation. They act on neurons in themyenteric plexus as mu-opioid receptor agonists, leading to decreased GImotility and propulsion. The proportion of the US adult population whotake opiates chronically (non-cancer patients), is roughly 4%. In anobservational study of patients on opiates for chronic pain, 47%experienced constipation (Tuteja et al. 2015 Neurogastroenterol Motil22: 424-430). There is evidence that chronic constipation can predisposeindividuals to benign GI neoplasms and colorectal cancer. The hypothesisfor this is that increased transit times allow for greater exposure ofthe GI mucosa to carcinogenic agents such as some bile acids.

Approximately 30% of cancer patients undergoing treatment/surgery and90% of advanced stage patients experience significant cancer pain andare most often treated with opioids (Levy M H, Samuel T A. 2005. SeminOncol. 32:179-93), which in turn cause constipation in up to 90% ofpatients (Ahmedzai et al. 2015. Supp Care Cancer 23:823-830). Despitethis side effect, opioids are the most efficacious analgesics in thissetting. Dose limitation of opioids in cancer patients due toside-effects may result in a lack of adequate pain management.

Chemotherapeutic agents themselves can cause constipation. Vincaalkaloids, platinum agents, thalidomide and hormonal agents result in ahigh incidence of constipation (Gibson, Rachel J., and Dorothy M KKeefe. “Cancer chemotherapy-induced diarrhoea and constipation:mechanisms of damage and prevention strategies.” Supportive Care inCancer 14.9 (2006): 890-900).

Several drug toxicities affecting GI motility (e.g. causing constipationor diarrhea) in cancer are also related to or associated with otherimmune imbalances and nutritional imbalances. In this study, mice (maleICR; CD-1, 6-7 weeks old, 25-30 grams; Charles River Laboratories,Wilmington, MA) were individually housed. Mice were treated with eithercommercially-available fiber polydextrose (PDX; “Litesse”, DupontDanisco, Surrey, United Kingdom) or xylo-oligosaccharide (XOS;“Llife-Oligo XOS”, Bio Nutrition, Inc., Island Park, NY) or novel glycancompositions (xyl100, ara100, glu100); all administered at 1% ad libitumin drinking water for 11 days. A control group received plain drinkingwater. On day 12, all mice were administered morphine at a dose of 3mg/kg subcutaneously to reduce colonic propulsion. One control group ofmice were treated with naloxone, a mu-receptor inverse agonist 30minutes prior to morphine administration. Naloxone is known tocounteract the action of morphine at the mu-receptor. Colonic propulsionwas assessed as follows: thirty minutes post morphine dosing, a 3 mmglass bead was inserted at a depth of 2 cm into the distal colon througheach mouse's anus. Mice were observed for 30 minutes for expulsion ofthe bead, and the time in seconds to expulsion was noted. A cutoff of 30minutes was used as a maximum time.

Administration of naloxone, XOS and PDX had significant effects on thetime to bead expulsion, with overall latency decreased (FIG. 19 ).Xyl100-treated animals had an overall average decrease in expulsiontime, but this did not reach significance. Naloxone, XOS andxyl100-treated groups, fell into two groups, those mice that respondedand ones that responded significantly less to the treatments. Thiseffect was seen less in the PDX-treated animals. Seventy-five percent ofmice in the vehicle-treated group reached the maximal cutoff time.Ara100 and glu100 had a non-statistically significant effect on beadexpulsion.

A second analysis was performed using a reduction in expulsion of >25%of maximum expulsion time as a cutoff to define a “responder” (1350seconds)). Using this arbitrary cutoff, naloxone had 6/8 mice respond totreatment, PDX, 7 had responders, XOS had 5 responders, and xyl100 andara100 had 4 responders each, and glu100 and vehicle had 1 responder.

A third analysis was performed to determine the average time to beadexpulsion in the responder versus non-responder animals in eachtreatment group (FIGS. 20 a and 20 b ). A cutoff time for bead expulsionwas set at 1800 seconds. In this mouse model of colonic propulsion,naloxone had the expected effect of reversing the effects of morphine,as it is a direct inverse agonist, competing with morphine formu-receptor occupancy and blocking its known effects on gastrointestinalmotility. XOS and PDX have been shown to have efficacy in clinicalconstipation settings (Shimada et al, 2015 J. Nutr Sci Vitaminol61:345-353; Tateyama et al., 2005 J Nutr Sci Vitaminol 51:445-448), andhad positive effects in this mouse study. Xyl100, XOS and naloxone hadan effects in this model and PDX and ara100 had similar effects as well,especially when the group of responders was assessed (FIG. 20 b ).

These results, obtained in a widely used animal model for colonicpropulsion suggest that glycan therapeutics reduced morphine's effect ofdecreased colonic motility, as measured by colonic propulsion. Selectedglycans appear to increase colonic propulsion in animals responsive totreatment, whereas some animals were not responsive.

Example 21: Effect of Glycans on Cancer Development in a Mouse MelanomaModel

To study efficacy of the therapeutic glycans described herein in thetreatment of cancer, an animal model of melanoma was chosen. In thismodel, mice usually develop tumors within 7-21 days and a treatmenteffect can be observed by measuring the kinetics of tumor growth. Forexample, a treatment effect can be in the form of delaying tumor growth.

Melanoma is a cancer of the skin, but is mostly observed in skin exposedto sunlight. Melanoma is most commonly diagnosed in non-Hispanic whites;1 per 100,000 in African Americans, 4 per 100,000 in Hispanics, and 25per 100,000 in non-Hispanic whites. The number of deaths in 2015 was 2.7per 100,000 men and women per year. The rates of melanoma have beenrising for at least 30 years. The estimated 5-year survival rate forpatients whose melanoma is detected early is about 98 percent in theU.S. The survival rate falls to 63 percent when the disease reaches thelymph nodes, and 17 percent when the disease metastasizes to distantorgans.

New checkpoint inhibitor therapies have improved the outlook forpatients with metastatic melanoma. Anti-PD-1 therapies (e.g. nivolumaband pembrolizumab) have been shown to produce overall response rates onthe order of 30% in metastatic melanoma patients (nivolumab FDA labeland pembrolizumab FDA label). Combination studies of anti-PD-1 therapywith anti-CTLA4 therapy have shown 60% overall response rate (comparedto 11% with anti-CTLA4 therapy alone) and a median progression-freesurvival of 8.9 months (nivolumab FDA label). Larkin et al. showedmedian progression-free survival among stage III and IV metastaticmelanoma patients of 11.5 months for combination therapy of nivolumab(anti-PD-1) and ipilimumab (anti-CTLA4) compared to 6.9 months fornivolumab alone, and 2.9 months for ipilimumab alone (DOI:10.1056/NEJMoa1504030).

Some commensal bacterial species may be implicated in regulating gutimmunity and responses to immunotherapies in physically distant tumors(Vétizou M et al. Anticancer immunotherapy by CTLA-4 blockade relies onthe gut microbiota. Science 2015 Nov. 27; 350:1079). Sivan et al. showeddecreased tumor growth kinetics of B16 melanoma cells in mice bycombining bifidobacteria species with anti-PD-L1 therapy (Sivan A et al.Commensal Bifidobacterium promotes antitumor immunity and facilitatesanti-PD-L1 efficacy. Science 2015 Nov. 27; 350:1084). Therapeuticglycans capable of modulating the microbiota (such as, e.g.,Bifidobacterium, Bacteroidales, Clostridiales) may be useful in cancertherapy, in some cases by promoting anti-tumor immunity, in some casesby increased melanoma-specific effector T-cell responses. Therapeuticglycans combined with existing immunotherapies may produce an additiveor synergistic effect. Cancer models, such as the animal melanoma modelare informative with respect to efficacy of agents for the treatment ofimmune imbalances and/or nutritional imbalances.

Melanoma Cell Line

B16.F10.SIY cells were cultured at subconfluence in Dulbecco's ModifiedEagle's Medium with (DMEM) supplemented with 10% fetal bovine serum(FBS) and standard Pen/Step supplement (Life Technologies). Cellexpression of GFP-SIY fusion was ascertained via flow cytometry andcells were only injected if >90% of cells were positive for SIY peptideexpression. Cells were trypsinized and counted, and cell viabilitydetermined via trypan blue exclusion assay prior to injection.

Mouse Model of Melanoma

Six to eight week old female C57BL/6 mice were acquired from Taconic,housed under SPF conditions, and fed a chow of Harlan Teklan 2018 adlibitum. At the beginning of the study, a total of 1×10{circumflex over( )}6 cells of the syngeneic melanoma cell line B16.F10.SIY wereinjected subcutaneously into each of the mice. Tumor size was measuredtwice per week by multiplying length times the square of the width times0.5.

Glycans were dissolved in the drinking water of the mice at aconcentration of 1%. Mice were divided into five treatment groups: (1)no treatment (n=15); (2) man100 administered from 5 days prior to thesubcutaneous injection of the tumor cell line through to when tumor sizeexceeded 1500 mm{circumflex over ( )}3 (n=10); (3) no glycan andsubcutaneous injection of 100 ug an anti-mouse anti-PD-L1 antibody (e.g.clone 10f.9g2 from BioXCell) at days 7, 10, 13, 16, 19, 22, 25, 28post-tumor implantation (n=15); (4) 1e9 CFU of Bifidobacterium mixture(e.g. B. bifidum, B. longum, B. lactis, and B. breve probiotic mixturefrom Seeking Health) administered by oral gavage on days 7 and 14post-tumor implantation (n=10); and (5) no treatment, but the normalHarlan Teklan 2018 diet was replaced with a modified AIN-93G diet thathad dietary fiber replaced with free glucose (n=10). The anti-PD-L1group was included as a control group, as anti-PD-L1 has been previouslyshown to delay tumor growth kinetics in this mouse model of melanoma(Sivan A et al.).

FIG. 21 shows tumor growth curves for Group 1 mice that received vehicletreatment (gray long-dashed line) and Group 2 mice that received Man100in the drinking water at 1% from 5 days prior to tumor inoculationthrough the duration of the study (black solid line). As can be seen inFIG. 21 , the tumor growth curves were suppressed in mice that receivedman100 in the drinking water (Group 2) compared to the vehicle control(Group 1). Additionally, mice receiving anti-PD-L1 (Group 3) showedsuperior tumor growth suppression (gray shortest-dashed line), andaddition of the bifidobacteria mix (Group 4, gray medium-dashed line)did not show significant tumor growth changes compared to Group 1. Thiseffect was determined to be statistically significant (p<0.05) on days21, 24, 28, and 31 based on one-way ANOVA comparing Group 2 to Group 1.Man100 inducing a delay in tumor growth in this model suggests enhancedimmune control of the tumors throughout the duration of treatment.

FIG. 22 shows the spider plots of the individual tumor growth curves forGroup 1 (vehicle control, thin gray dotted lines), Group 2 (Man100,thick black solid lines), and Group 3 ( ), anti-PD-L1, thick gray solidlines). By day 24, the tumor growth in most of the animals in Group 1became exponential, whereas in Group 2 and Group 3, the exponentialphase was delayed until days 28 or 31 for almost all of the animals.Since delay of tumor growth was achieved with both man100 andanti-PD-L1, but both groups relapsed, it suggests the possibility ofadditive or synergistic effects of combining man100 with anti-PD-L1 tosuppress tumor growth or induce robust tumor rejection. Man100 couldalso be combined with other therapies to produce an additive orsynergistic effect.

Example 22: Glycan Treatment in Patients with Melanoma

Patients diagnosed with metastatic melanoma are randomized to receiveeither 12 g per day of a glycan (dissolved in water and administeredorally) or placebo for the full duration of standard-of-care therapy.Every month, tumor size is determined by CT scan, or where notavailable, by caliper measurement or X-ray. Every month, fecal samplesare collected for analysis. Every 8 weeks, tumor biopsies are taken foranalysis, including histology and microscopy to quantifytumor-infiltrating lymphocytes (TIL). Tumor size measurements, fecalsamples, and tumor biopsies are taken at baseline prior to any therapy.

Fecal samples are expected to reveal that treatment with glycanincreases the absolute and relative proportion of Bifidobacteriumspecies in the feces.

Tumor biopsies are expected to reveal that treatment with glycanincreases the proportion of TIL from baseline, and the magnitude ofincrease is larger than the placebo group.

On average, the glycan-treated patients are expected to experience lesstumor growth over the period of treatment than the placebo controls.

Example 23: Glycan Treatment in Patients with Prostate Cancer

Patients diagnosed with prostate cancer are randomized to receive either12 g per day of a glycan, dissolved in water and administered orally, orplacebo for the full duration of standard-of-care therapy. Every month,fecal samples are collected for analysis. Every 8 weeks, tumor biopsiesare taken for analysis, including histology and microscopy to quantifytumor-infiltrating lymphocytes (TIL). Tumor biopsies are taken atbaseline prior to any therapy.

Fecal samples are expected to reveal that treatment with glycanincreases the absolute and relative proportion of Bifidobacteriumspecies in the feces.

Tumor biopsies are expected to reveal that treatment with glycanincreases the proportion of TIL from baseline, and the magnitude ofincrease is larger than the placebo group.

Patients that experience an increase in TIL from baseline then receive 3mg/kg of anti-CTLA4 therapy intravenously every 3 weeks for a total offour doses. Every month, tumor size is determined by CT scan, or wherenot available, by caliper measurement or X-ray. Every month, fecalsamples are collected for analysis. Every 8 weeks, tumor biopsies aretaken for analysis, including histology and microscopy to quantifytumor-infiltrating lymphocytes (TIL). Tumor size measurements, fecalsamples, and tumor biopsies are taken at baseline prior to any therapy.

Fecal samples are expected to reveal that treatment with glycanincreases the absolute and relative proportion of Bifidobacteriumspecies in the feces.

Tumor biopsies are expected to reveal that treatment with glycanincreases the proportion of TIL from baseline, and the magnitude ofincrease is larger than the placebo group.

On average, the glycan-treated patients experience less tumor growthover the period of treatment than the placebo controls.

Example 24: Properties of the Glycan Therapeutic in the Treatment,Co-Treatment and Prevention of Different Oncological Processes/Diseases

In a group of mice that take a selected test glycan therapeutic arepression of the expression of oncogenes jun, myc and fos may bedetected with respect to the control group. The jun and fos products aretranscription factors that dimerize to form the transcription complexcalled AP-1 (Activating Protein-1). AP-1 is a transcription factor thatregulates expression of genes induced by growth factors and tumorpromoters. Overexpression of oncogenes Jun and/or fos is associated withseveral cancers such as breast, ovarian, colon, osteosarcoma, cervical,lung and bladder cancer. Therefore, AP-1 is used as a target forchemotherapeutic treatment of cancer. Myc oncogene product is a proteinthat regulates the expression of the transcription factor E2F andphosphatase responsible for activation of Cdc cyclins, which areinvolved in cell cycle regulation. The myc oncogene is overexpressed inmany human cancers, including pancreatic, cervical, breast and coloncancer. Myc oncogene product is also used as target for cancertreatment. A study in humans showed that in the intestinal mucosa thereis a repression in the expression of oncogenes jun, fos and myc afterinfusion of the membrane with a strain of Lactobacillus. In a group ofmice that take a selected test glycan therapeutic a repression on theexpression of the gene Adamts1 (a disintegrin-like and metalloproteinase(reprolysin type) with thrombospondin type 1 motif) may be detected withrespect to the control group. Adamts1 gene product is a protein that hasa metalloproteinase domain and disintegrin domain. This protein isinvolved in inflammatory processes and the development of cancercachexia as tested in animal models of colon cancer. It has beendemonstrated overexpression of Adamts1 gene in breast cancer with highmetastatic activity. It has been speculated that overexpression of thisgene might promote tumor growth by recruiting fibroblasts. In a group ofmice that take a selected test glycan therapeutic a repression on theexpression of the gene ATF3 (activating transcription factor 3) may bedetected with respect to the control group. ATF3 gene product is atranscription factor expressed in conditions of stress and DNA damage invarious tissues. In many breast tumors has been reported overexpressionof ATF3. This protein is used as a marker of prostate cancer since itsinvolvement has been shown in developing this type of cancer and istherefore a potential therapeutic target. In a group of mice that take aselected test glycan therapeutic an activation on the expression ofDdit4 gene (DNA-damage-inducible transcript 4) may be detected withrespect to the control group.Ddit4 gene product is a protein calledRTP801 or REDD1, which inhibits the pathway mTOR/S6K1, involved in cellproliferation. Inhibitors of this route are being evaluated as cancertherapy. In mice has been described that the gene Ddti4 deficiencypromotes tumor growth, while in humans has been described repression ofthe gene in various cancers. In a group of mice that take a selectedtest glycan therapeutic a repression on the expression of Egr1 gene(early growth response 1) may be detected with respect to the controlgroup. The Egr1 gene product is a transcription factor involved invarious cellular processes and its involvement has been demonstrated incell growth and survival of prostate cancer. In animal models ofprostate cancer has shown that lack of Egr1 gene retards tumor growth.In a group of mice that take a selected test glycan therapeutic arepression on the expression of Sox9 gene (SRY (sex Determining RegionY)-box 9) may be detected with respect to the control group. The Sox9gene produces a protein that acts as a transcription factor withDNA-binding domain type HMG (High Mobility Group). It has been shown animplication of Sox9 gene product in the proliferation of pancreaticcancer and overexpression of the same in different cell lines of coloncancer. In a group of mice that take a selected test glycan therapeutica repression of the expression of interleukin 1 alpha gene (IL1a) may bedetected with respect to the control group. The IL1a is a cytokineinvolved in inflammatory processes. The IL1a gene is overexpressed invarious cancers, including lung cancer, colon and melanoma. In coloncancer IL1a stimulates the cell migration and angiogenesis and itsexpression is induced by prostaglandin E2. In a study in humans showedthat in the intestinal mucosa occurs a repression in the IL1a geneexpression after the infusion of the membrane with a strain ofLactobacillus. In a group of mice that take a selected test glycantherapeutic an activation of the expression of Gadd45b gene (growtharrest and DNA-damage-inducible 45 beta) and Gadd45q gene (growth arrestand DNA-damage-inducible 45 gamma) may be detected with respect to thecontrol group. The products of Gadd45g and Gadd45b genes are proteinsrelated with cell cycle control. In mice models of melanoma have beenshown that a lack of function of Gadd45b produces higher tumor growth.The product of this gene is required for activation of p38 kinase. Thep38 protein is involved in tumor suppression. The expression of Gadd45gand Gadd45b genes is repressed in various cancers.

TABLE 1 Genus level Microbial Constituents of the GI tract. Phylum ClassGenus Actinobacteria Actinobacteria Actinomyces, Adlercreutzia,Atopobium, Bifidobacterium, Collinsella, Corynebacterium, Eggerthella,Mobiluncus, Propionibacterium, Rothia, Slackia Bacteroidetes BacteroidiaAlistipes, Bacteroides, Dysgonomonas, Odoribacter, Parabacteroides,Porphyromonas, Prevotella, Tannerella Flavobacteria CapnocytophagaFirmicutes Bacilli Bacillus, Enterococcus, Gemella, Granulicatella,Lactobacillus, Lactococcus, Staphylococcus, Streptococcus, Turicibacter,Weissella Clostridia Acidaminococcus, Anaerococcus, Anaerofilum,Anaerofustis, Anaerostipes, Anaerotruncus, Anaerovorax, Bacteroides,Bacteroides, Blautia, Clostridium, Coprococcus, Dehalobacterium,Dialister, Dorea, Eubacterium, Faecalibacterium, Finegoldia,Lachnobacterium, Lachnospira, Megamonas, Megasphaera, Mitsuokella,Moryella, Oribacterium, Oscillospira, Peptococcus, Peptoniphilus,Peptostreptococcus, Phascolarctobacterium, Pseudobutyrivibrio,Roseburia, Ruminococcus, Ruminococcus, Selenomonas, Subdoligranulum,Veillonella Fusobacteria Fusobacteria Fusobacterium, LeptotrichiaBetaproteobacteria Comamonas, Herbaspirillum, Lautropia, Neisseria,Oxalobacter, Sutterella Deltaproteobacteria Bilophila, Desulfovibrio,LE30 Epsilonproteobacteria Campylobacter, HelicobacterGammaproteobacteria Actinobacillus, Aggregatibacter, Citrobacter,Escherichia, Haemophilus, Klebsiella, Moraxella, Pseudomonas, RaoultellaSpirochaetes Spirochaetes Treponema Synergistetes SynergistetiaCloacibacillus, Synergistes Tenericutes Erysipelotrichi Bulleidia,Catenibacterium, Clostridium, Coprobacillus, Holdemania, RFN20Mollicutes Asteroleplasma, Mycoplasma Verrucomicrobia VerrucomicrobiaeAkkermansia Euryarchaeota Methanobacteria Methanobrevibacter

TABLE 2 Microbial Metabolites 2-hydroxyisobutyrate,3-hydroxyisovalerate, 3-methyl-crotonyl- glycine,3-methylcrotonylglycine, allantoin, betaine, formate, mannitol, p-cresolglucuronide, phenylacetylglycine, sarcosine, taurine, acetic acid,acetylaldehyde, ascorbic acid, butanedione, butyric acid, deoxycholicacid, ethylphenyl sulfate, formic acid/ formate, indole, isobutyricacid, isovaleric acid, propionic acid, serotonin, succinicacid/succinate, TMAO, tryptophan, valeric acid, ursodeoxycholic acid,lactate, lactic acid, hydrogen peroxide

TABLE 3 Genus level microbial constituents predominant in the largeintestine (compared to small intestine) in healthy humans. Phylum ClassGenus Bacteroidetes Bacteroidia Bacteroides, Butyricimonas, Odoribacter,Parabacteroides, Prevotella Firmicutes Clostridia Anaerotruncus,Phascolarctobacterium, Ruminococcus, Proteobacteria DeltaproteobacteriaBilophila Verrucomicrobia Verrucomicrobiae Akkermansia

TABLE 4 Genus level microbial constituents predominant in the smallintestine (compared to large intestine) in healthy humans. Phylum ClassGenus Actinobacteria Actinobacteria Cryocola, Mycobacterium FirmicutesBacilli Enterococcus, Lactococcus, Streptococcus, TuricibacterClostridia Blautia, Coprococcus, Holdemania, PseudoramibacterEubacterium Proteobacteria Alphaproteobacteria Agrobacterium,Sphingomonas Betaproteobacteria Achromobacter, Burkholderia, Ralstonia

EQUIVALENTS AND SCOPE

This application refers to various issued patents, published patentapplications, journal articles, and other publications, all of which areincorporated herein by reference. If there is a conflict between any ofthe incorporated references and the instant specification, thespecification shall control. In addition, any particular embodiment ofthe present invention that falls within the prior art may be explicitlyexcluded from any one or more of the claims. Because such embodimentsare deemed to be known to one of ordinary skill in the art, they may beexcluded even if the exclusion is not set forth explicitly herein. Anyparticular embodiment of the invention can be excluded from any claim,for any reason, whether or not related to the existence of prior art.

Those skilled in the art will recognize or be able to ascertain using nomore than routine experimentation many equivalents to the specificembodiments described herein. The scope of the present embodimentsdescribed herein is not intended to be limited to the above Description,Figures, or Examples but rather is as set forth in the appended claims.Those of ordinary skill in the art will appreciate that various changesand modifications to this description may be made without departing fromthe spirit or scope of the present invention, as defined in thefollowing claims.

The invention claimed is:
 1. A method for reducing inflammation of agastrointestinal inflammatory disease in a subject having an immuneimbalance, comprising administering to the subject an effective amountof a composition comprising a glycan therapeutic preparation, wherein:i) the glycan therapeutic preparation comprises branched glycanscomprising glucose, galactose, arabinose, mannose, fructose, xylose,fucose, or rhamnose glycan units; ii) the glycan therapeutic preparationcomprises an average degree of branching (DB) of at least 0.01; iii) atleast 50% of the glycans in the glycan therapeutic preparation have adegree of polymerization (DP) of at least 3 and less than 30 glycanunits; and iv) the ratio of alpha- to beta-glycosidic bonds present inthe glycans of the glycan therapeutic preparation is between about 1:1to about 5:1; thereby reducing inflammation of the gastrointestinalinflammatory disease in the subject having the immune imbalance.
 2. Themethod of claim 1, wherein the composition further comprises a probioticmicroorganism.
 3. The method of claim 1, wherein the level of ashort-chain fatty acid (SCFA) is modulated in the subject uponadministration of the composition.
 4. The method of claim 3, wherein thelevel of the SCFA is increased.
 5. The method of claim 3, wherein theSCFA is one or more of acetate, propionate, and/or butyrate.
 6. Themethod of claim 1, wherein administration of the composition results inthe stimulation of growth or stimulation of activity of beneficial gutbacteria.
 7. The method of claim 1, wherein administration of thecomposition results in the stimulation of growth or stimulation ofactivity of Bacteroidetes, Prevotella, Ruminococcus, Parabacteroides,Firmicutes, Alistipes, Lachnospiraceae, and/or Ruminococcaceae.
 8. Themethod of claim 1, wherein administration of the composition results inthe modulation of one or more biomarkers and/or one or more cytokines.9. The method of claim 1, wherein administration of the compositionresults in the modulation of one or more biomarkers selected from thegroup consisting of: Interleukin 10, Interleukin, 4, Interleukin 13,Interleukin 35, C-reactive protein, interleukin-6, interleukin-8,interleukin-18, leptin, serum amyloid A, serum amyloid P, or tumornecrosis factor-alpha.
 10. The method of claim 1, wherein administrationof the composition results in the modulation of one or more cytokinesselected from the group consisting of: TNF-α, IL-8, monocytechemoattracting protein 1 (MCP-1), TGF-β, IL-12, IFN-γ, IL-4, IL-10,IL-1β, IL-6, IL-23, IL-17A, IL-17F, IL-22, and IL-13.
 11. The method ofclaim 1, wherein the immune imbalance is an aberrant activation of thesubject's immune system.
 12. The method of claim 1, wherein the immuneimbalance is chronic.
 13. The method of claim 1, wherein the immuneimbalance is local.
 14. The method of claim 1, wherein the immuneimbalance is accompanied by aberrant growth of a pathogenic cell. 15.The method of claim 14, wherein the pathogenic cell is an intracellularpathogen or an extracellular pathogen.
 16. The method of claim 14,wherein the pathogenic cell is an Escherichia coli, Klebsiellapneumoniae, Salmonella, Enterococcus, or Clostridium difficile cell. 17.The method of claim 1, wherein the gastrointestinal inflammatory diseaseis inflammatory bowel disease (IBD), ulcerative colitis (UC), graftversus host disease (GVHD), or psoriasis.
 18. The method of claim 1,wherein the immune imbalance is acute.
 19. The method of claim 1,wherein the immune imbalance is systemic.
 20. The method of claim 1,wherein add a claim wherein the method further comprises administeringan anti-inflammatory agent.
 21. The method of claim 1, wherein thegastrointestinal inflammatory disease is intestinal inflammation. 22.The method of claim 1, wherein the gastrointestinal inflammatory diseaseis drug-induced enteritis or colitis.